Below is my first cut at describing the options, as found in ultra.cfg...

set use_onegun 1
----------------
This option selects "one-gun" mode - which will soon be a seperate
DM server mod. It replaces all weapons with a "chosen" weapon, and
all ammo to the correct type for this weapon. Setting this value to 0
disables this option. 1 randomly chooses the weapon each level. Numbers
2 to 10 choose weapons (2=shotgun, 3=s.shotgun, 4=machinegun... 10=BFG).    

set lmctf 1
-----------
This option choses LMCTF mode - if you have the LMCTF pak file in
your eraser directory, you can use this for LMCTF support.  Note that
not all of the features are supported, but bots are randomly assigned
one of 27 male skins per team and one of 11 female skins per team.
To also change the rune models and sounds, exec lmctf_quick.cfg.

set invisible_dmstarts 1
------------------------------
Hides the DM starts for LMCTF mode.

set gamerules 2
-----------
This option enables Rogue DM tag gameplay.

set allow_func_explosives 1
---------------------------------------
Enables func_explosives to show up in maps that have them (unless
they have the not-in-deathmatch flag).  They will respawn 30 seconds
after being destroyed.  Players that are in the way will be gibbed.

set allow_disabled_func_explosives 1
----------------------------------------------
Enable func_explosvies that are disabled with the not-in-deathmatch cvar.

set allow_pickuprune 1
----------------------
Setting this cvar to 1 allows the player to pickup a rune previously
dropped (like Lithium/LMCTF). Setting to 0 doesn't allow the player to
pick them up again (like CTF)


set allow_flagdrop 1
--------------------
Setting this cvar to 1 allows the player to drop the flag using the
command "drop flag", LMCTF style. When this is set to 0, you get the
abuse that Zoid put into standard CTF.


set mapmod_random 1
-------------------
This sets the map-cycling to random mode. Note the difference in
the name from the Lithium standard (but the same as in Eraser).


set mapqueue "ultra-maps.txt"
-----------------------------
This selects where the maps to be used in the map cycle may be
found. 

set use_mapqueue 1
------------------
This option enables map-cycling.


set rune_resist_name "resist rune"
set rune_strength_name "strength rune"
set rune_haste_name "haste rune"
set rune_regen_name "regen rune"
set rune_vampire_name "vampire rune"
set rune_ammogen_name "ammogen rune"
---------------------------------------
These define the pickup names of the runes/techs/artifacts -
these can be used to simulate lithium/LMCTF naming conventions.


set rune_resist_shortname "resist"
set rune_strength_shortname "strength"
set rune_haste_shortname "haste"
set rune_regen_shortname "regen"
set rune_vampire_shortname "vampire"
set rune_ammogen_shortname "ammogen"
---------------------------------------
These define the name used for rune/tech/artifacts on the 
enhanced HUD.


set use_lithiumrunes 1
----------------------
This sets the colouring of the runes/techs/artifacts 
to Lithium-style runes - eg. pink = vampire etc.


set rune_resist_mdl "models/items/keys/pyramid/tris.md2"
set rune_strength_mdl "models/items/keys/pyramid/tris.md2"
set rune_haste_mdl "models/items/keys/pyramid/tris.md2"
set rune_regen_mdl "models/items/keys/pyramid/tris.md2"
set rune_vampire_mdl "models/items/keys/pyramid/tris.md2"
set rune_ammogen_mdl "models/items/keys/pyramid/tris.md2"
----------------------------------------------------------
These define the model used for the different techs. This
can be used to switch between piramid keys, and specific
models.


set rune_resist_icon "tech1"
set rune_strength_icon "tech2"
set rune_haste_icon "tech3"
set rune_regen_icon "tech4"
set rune_vampire_icon "tech5"
set rune_ammogen_icon "tech6"
----------------------------------------------------------
These define which icons to use for the techs in CTF mode.  They default to the pyramid key icon.  Use the above for CTF.  tech5.pcx is included in 3Team CTF.


set rune_resist_sound "world/force2.wav"
set rune_strength_sound "items/damage3.wav"
set rune_haste_sound "world/x_light.wav"
set rune_regen_sound "items/l_health.wav"
set rune_vampire_sound "makron/pain2.wav"
set rune_ammogen_sound "misc/spawn1.wav"
-------------------------------------------
These set the sounds that will be used for the
respective rune/tech's.


set use_runes 1
---------------
This enables the runes/techs/artifacts.

set rune_flags 63
-----------------
This sum of numbers tells the EraserULTRA which runes to spawn.
1= Resistance
2= Strength
4= Haste
8= Regen
16= vampire
32= Ammogen

set rune_perplayer 0.7
-------------------------------
This sets the number of runes per player to spawn.  At least one of
each rune type that is enabled will always be spawned.


set rune_max 15
----------------------
This sets the maximum number of runes that can be spawned.


set use_viewweapons 1
---------------------
This enables viewable weapons (broken?).


set motd "motd.txt"
-------------------
This defines where to find the message-of-the-day
text file. This is a simple (and small) text file that
is displayed to clients on joining the game.


set def_id 1
------------
This enables player-identification.


set def_hud 2
-------------

This enables the enhanced HUD when set to 2. Value 1
uses the standard HUD, and 0 has no HUD.
Value 3 uses the Lithium ammo HUD, and value 4 uses the Rogue/Xatrix sorted ammo HUD.


set def_scores 1
----------------
This enables the enhaned scoreboard - value 0 provides
a standard scoreboard, while 1 provides an improved
scoreboard sorted by frags, and 2 sorts by FPH.


set mega_gibs 1
----------------
Enables tons of bouncy, squishy gibs.  Set to 0 to disable if you get overflowed.


set player_gib_health -40
----------------
Set the player gib health threshold.  Lower means bodies take more damage to gib.


set knockback_adjust 1.5
set knockback_self 2.0
-------------------------
These adjust the ammount of knockback caused to
others/yourself when using some weapons - adjusting
these affects height of rocket-jumps, and recoil etc.


set sk_fall_damagemod 0.9
----------------------
This value adjusts the amount of damage caused by
falling long distances.


set rune_life 20
----------------
This variable changes the amount of time a rune will
last for if not picked up.


set rune_resist 2.0
-------------------

Adjusts how much the "resist" rune/tech will shield
the player.


set rune_strength 2.0
---------------------
Adjusts by how much damage is increased when using
the strength rune/tech.


set rune_regenmax 200
---------------------
Adjusts the maximum health when using a regen
rune/tech.


set rune_vampire 0.5
--------------------
Adjusts how much of the damage inflicted is added
to a player when using the vampire rune/tech.


set rune_vampiremax 200
-----------------------
Adjusts the maximum health that can be gained when
using the vampire rune/tech.


set use_hook 1
--------------
This enables the grappling hook.


set sk_hook_offhand 1
--------------
This enables the offhand grappling hook.


set sk_new_hand_hook 
---------------------
This enables the new hand grapple sounds, allowing you to have
both the offhand grapple and the original CTF grapple.


set sk_hook_style 0
--------------
Set to 1 for a laser hook offhand hook, 0 for a regular offhand hook.


set grapple_mdl "set grapple_mdl "models/objects/grenade2/tris.md2"
--------------
Sets the model to use for the grappling hook.  You can also use "models/weapons/grapple/hook/tris.md2"
for the CTF hoof if you have CTF installed.


set sk_hook_speed 1000
-------------------
Sets how fast the grappling hooks are thrown.


set sk_hook_pullspeed 800
----------------------
Sets how fast the grappling hook pulls the player.


set sk_hook_sky 0
--------------
Sets whether the grappling hook may stick to the
sky texture or not.


set sk_hook_maxtime 5.0
--------------------
Sets the maximum amount of time that a player can
"hang" on the grappling hook.


set sk_hook_damage 2
-----------------
Sets how much damage is caused when a player is
"hit" with the grapple.


set sk_start_health 100
--------------------
This sets the amount of health given to a player
on spawning.


set sk_start_bullets 200
set sk_start_shells 10
set sk_start_rockets 5
set sk_start_grenades 1
set sk_start_cells 50
set sk_start_slugs 5
--------------------
These variables set the amount of ammo given to
the player on spawning.


set sk_max_health 120
set sk_max_armor 200
set sk_max_bullets 200
set sk_max_shells 100
set sk_max_rockets 50
set sk_max_grenades 50
set sk_max_cells 200
set sk_max_slugs 50
set sk_max_magslugs 50
set sk_max_flechettes 200
set sk_max_rounds 150
set sk_max_prox 50
set sk_max_tesla 50
set sk_max_traps 20
-------------------
These variables set the maximum amount of ammo
that a player may carry (without a pack).

set sk_bando_bullets 300
set sk_bando_shells 150
set sk_bando_cells 300
set sk_bando_slugs 75
set sk_bando_magslugs 75
set sk_bando_flechettes 300
set sk_bando_rounds 225
--------------------
These variables set the maximum amount of ammo
that a player may carry (after picking up a bandolier).

set sk_pack_health 120
set sk_pack_armor 200
set sk_pack_bullets 400
set sk_pack_shells 200
set sk_pack_rockets 100
set sk_pack_grenades 100
set sk_pack_cells 400
set sk_pack_slugs 100
set sk_pack_magslugs 100
set sk_pack_flechettes 400
set sk_pack_rounds 300
set sk_pack_prox 100
set sk_pack_tesla 100
set sk_pack_traps 50
--------------------
These variables set the maximum amount of ammo
that a player may carry (after picking up a pack).

set sk_armor_bonus_value 2
------------------
Sets the value of the armor shards.

set sk_health_bonus_value 2
------------------
Sets the value of the stimpacks.

set sk_powerup_max 2
------------------
Sets how many powerups of each type you can collect.

set sk_doppleganger_max 2
------------------
Sets how many doppelgangers you can collect.

set sk_nuke_max 1
------------------
Sets how many A-M bombs you can collect.

set sk_defender_time 30
set sk_vengeance_time 30
set sk_hunter_time 30
set sk_doppleganer_time 30
set sk_quad_time 30
set sk_inv_time 30
set sk_breather_time 30
set sk_enviro_time 30
set sk_silencer_shots 30
set sk_ir_time 30
set sk_double_time 30
set sk_quad_fire_time 30
------------------
Sets the duration of the powerups.


set sk_start_weapon 0
------------------
Chooses which weapon will be used (if available)
on starting - 0 chooses best weapon, 1 chooses
blaster, 2 chooses shotgun, etc.


set sk_start_blaster 1
set sk_start_shotgun 0
set sk_start_sshotgun 0
set sk_start_machinegun 1
set sk_start_chaingun 0
set sk_start_grenadelauncher 0
set sk_start_rocketlauncher 0
set sk_start_hyperblaster 0
set sk_start_railgun 0
set sk_start_bfg 0
set sk_start_ionripper 0
set sk_start_phalanx 0
set sk_start_etfrifle 0
set sk_start_proxlauncher 0
set sk_start_plasmabeam 0
set sk_start_disruptor 0
set sk_start_chainfist 0
set sk_start_plasmarifle 0
---------------------------
These variables allow any weapon to be given to
the player upon spawning. If the blaster is not
given, then this weapon is not available.


set sk_no_shotgun 0
set sk_no_sshotgun 0
set sk_no_machinegun 0
set sk_no_chaingun 0
set sk_no_grenadelauncher 0
set sk_no_rocketlauncher 0
set sk_no_hyperblaster 0
set sk_no_railgun 0
set sk_no_bfg 1
set sk_no_ionripper 0
set sk_no_phalanx 0
set sk_no_traps 1
set sk_no_etfrifle 0
set sk_no_proxlauncher 0
set sk_no_plasmabeam 0
set sk_no_disruptor 1
set sk_no_chainfist 0
set sk_no_plasmarifle 0
set sk_no_quad 0
set sk_no_pent 1
set sk_no_mines 1
set sk_no_nukes 1
set sk_no_spheres 1
-------------------------
These variables inhibit the respective weapons
from spawning - allowing weapons to be banned.


set sk_power_armor_screen 0.25
set sk_power_armor_shield 0.50
---------------------------
These set how much the power armour shields the
player.


set fast_respawn 0.75
---------------------
This sets how much faster items will respawn, for
each player in the game (ie. the more players, the
faster they respawn). This is currently too fast.


set fast_pbound 16
------------------
This limits the maximum number of players for
the purposes of fast_respawn - so when playing a
64 player game items will not respawn instantly.


set use_safety 1
----------------
Enables safety-mode. Safety mode prevents players
from being hurt until either the safety-time runs
out, or they shoot a weapon.


set safety_time 10.0
--------------------
This sets how long after spawning a player is in
safety mode.


set use_observer 1
------------------
This enables observer mode on starting - to enter
the game, simply hit fire.

(weapon balancing)
------------------

These options (too many to list) allow the user to
tweak the settings of weapons - eg. to the "pro-rocket"
settings as per quake1, or to make very powerful blasters.

set intermission_time 8.5  
-------------------------
Sets the minimum amount of time before the intermission ends.


set intermission_sound "world/xian1.wav"
----------------------------------------
Defines which sound is to be played on reaching the intermission.


set dm_config "dm_config.cfg"
set ctf_config "ctf_config.cfg"
-----------------------------
These define which config file should be executed when starting
a DeathMatch or CTF game. This allows a different configuration
for both game-types - for example, a higher frag-limit in CTF.


replace ammo_cells ammo_slugs
-----------------------------
This command replaces any given item with any other - as
long as both item names are valid. The replacement will take
effect after the next map change. This can be used to replace
the BFG with a railgun, rather than banning it (which often
unbalances the level).

Note that this command only takes effect after a level change,
but the replace-list is cleared when using the "map" command
- so make sure that you change level useing "gamemap q2dm1".
Also note that you shouldn't put this in an autoexec.cfg, and
be aware that putting too many replace commands in the
dm/ctf_config.cfg files will cause the game not to restart
correctly.

replace_list
------------
This command allows you to view the current replace list,
so you can see before changing levels what will be replaced
with what (for typo detection).