Server Commands:

g_grapplespeed (default 1800)
Determines how fast the grappling hook flies

g_grapplepullspeed (default 1200)
Determines how fast the grapple pulls players along

g_grappledelay (default 400)
The minimum number of milliseconds between grapples. In other words, the reload time of the grapple.

g_reloadfactor (default 1)
A number usually between 0 and 1 that is multiplied against the reload time. 0 is no reload time, 1 is normal. Settings below 0.5 are not recommended, as reload times will quickly start to become framerate-dependent for some weapons. (For example, if it is set to 0.5, the lightning gun will not fire as quickly for players whose framerates are below 40.) You can get around this by using pmove_fixed.

This setting is probably most useful in instagib (instafreeze?) mode. Here is a list of reload times for the various weapons:

Gauntlet: 0.4 (2/5) seconds
Machinegun: 0.1 (1/10) seconds
Shotgun: 1 second
Grenade Launcher: 0.8 (8/10) seconds
Rocket Launcher: 0.8 (8/10) seconds
Lightning Gun: 0.05 (1/20) seconds
Railgun: 1.5 (1 1/2) seconds
Plasmagun: 0.1 (1/10) seconds
BFG: 0.2 (1/5) seconds

So if you wanted the railgun to reload every 1 second, you would set g_reloadFactor to 0.666.

g_railjumpknock (default 0)
Determines the strenght of the knockback of the Railgun. This only affects the player that fired the shot. Setting this to 100 will give a knockback equal to that of the Rocket Launcher. This allows making rail jumps.

g_thawtime (default 3)
The amount of time, in seconds, a player must stand next to a teammate to thaw him. Fractional values (e.g. 2.5) are fine.

g_autothawtime (default 150)
The amount of time, in seconds, it takes for a player to thaw automatically. Whole numbers only.

g_noDamageTime (default 0)
The amount of time, in seconds, that a player cannot be damaged after he spawns in. Fractional values are fine.

g_noFreezeTime (default 2)
The amount of time, in seconds, that a player cannot be frozen after he spawns in. Fractional values are fine.

g_noVoiceChatSounds (default 0)
Set this to "1" if you run a server and your players abuse the voice chat sounds. Players will no longer hear the voice chat sounds.

g_delagHitscan (default 1)
Leave this set to "1." Setting it to "0" will disable the lag compensation.

ref_password (default "")
Set it if you want a referee. Players can use the ref command to authenticate as referee using this password.
If set to "" players cannot authenticate as referee.

g_maxTimeout (default 120)
Maximum time of a team timeout in seconds

g_numTimeouts (default 3)
Maximum number of team timeouts per team per game

g_readyPercent (default 50)
Percent of all players needed to be ready to start

g_doTimeouts (default 0)
Set to "1" if you want teams to be able to call timeouts

g_doReady (default 0)
Set to "1" if you want players to have to ready up

g_doTeamLocks (default 0)
Set to "1" if you want teams lockable

g_allowFreeFloat (default 1)
Set to "0" if you'd rather not have frozen players free-float as spectators.

g_allowFollowEnemy (default 1)
With this set to “1,” when another an enemy rails a corpsicle or hits one with the gauntlet, the player whose corpsicle it is will spectate the enemy player. Set this to “0” if you'd rather not have that happen.

g_allowThirdPerson (default 1)
Set to "0" if you don't want players to be able to play in third-person mode.

g_grapple (default 0)*
Set this to "1" to enable the grappling hook on the server.

g_startArmor (default 0)*
Use to set the amount of armor a player will spawn with

disable_item_<item> (default 0)*
Set this to "1" to remove specific powerups from the game. Replace <item> with the full name of the item. Setting disable_item_quad to "1" will remove the Quad Damage from the game

dmflags (default 0)*
Uses a binary mask to set certain properties of the server. Add up all the numbers in front of the features you wish to enable and set dmflags to that value.

(8) - No Falling Damage.
(16) - Fixed Field of View (players' cg_fov will be locked at 90)
(32) - No footsteps. Footsteps will not be audible when a player is running
(64) - No Item Reset. When used, means that when a team wins a round all the living players will not have their health and weapon ammo reset. This would leave them at a disadvantage as the entire enemy team will be coming in fresh.
(128) - No Team Reset. This means that when a round is won, only the losing team will be unfrozen. The winning team still may have a few people that are frozen and that need to be saved. This will also leave the winning team at a disadvantage conceivably.
(256) - Weapons Stay. Weapons will not disappear when picked up.
(512) - No Playerclip. Players can move through so-called "clip brushes", invisible brushes which are used to close certain areas off.
(1024) - Nightmare Mode. This is a special setting players had asked be put in. It is basically hyper-Freeze Tag. All weapons do mega-damage with lots of starting ammo. It's Freeze on steroids. Note that with weaponlimit (see below) set to 2048, the Gauntlet will not do super damage. Thaw time and auto-thaw time are still set through g_thawtime and g_autothawtime.
(2048) - No Self Damage.

example: For a"nightmare mode" server with no footsteps and no falling damage, dmflags would be set to 1044 (8 + 32 + 1024)

wpflags (default 1)*
Uses a binary mask to determine what weapons players will spawn with.

(1) - Machinegun
(2) - Shotgun
(4) - Grenade Launcher
(8) - Rocket Launcher
(16) - Lightninggun
(32) - Railgun
(64) - Plasmagun
(128) - BFG10K
(256) - Nailgun (team arena only)
(512) - Prox Launcher (team arena only)
(1024) - Chaingun (team arena only)

example: For a server on which players would spawn with MG, SG and RG, dmflags would be set to 35 (1 + 2 + 32)

weaponlimit (default 0)*
Uses a binary mask to remove weapons and the ammo from a map. Uses the same values as wpflags.

votelimit (default 0)*
Uses a binary mask to disable commands which can be voted for.

(1) - map_restart
(2) - nextmap
(4) - map
(8) - g_gametype
(16) - kick
(32) - clientkick
(64) - g_dowarmup
(128) - timelimit
(256) - fraglimit
(512) - g_grappe

example: for a server on which players should not be able to vote for a certain map and shouldn't be able to change the timelimit, votelimit should be set to 132 (4 + 128).

Client Commands:

cg_iceChips (default 1)
Set to 1 to disable ice chips for faster framerates - though not much faster. You can also set this in the SETUP->GAME OPTIONS menu.

cg_delag (default 1)
Set this to "0" if you'd rather not have the server compensate for your ping. This setting is only meaningful if the server is compensating for lag (see g_delagHitscan). You can also set this in the SETUP->GAME OPTIONS menu.

cg_chatFilter (default 0)
Set this to "1" if you want player chats filtered for profanity.

cg_drawFrozen (default 1)
Set this to "0" if you'd rather not have your "% Frozen" or "% Thawed" indicator drawn when you are frozen.

cg_predictRailTrails (default 1)
It's probably useless, but set this to "0" if you'd rather not have your railgun appear to fire immediately. This setting is only meaningful if both cg_delag and g_delagHitscan are set to "1."

ready
Signals the server that you're ready

notready
Signals the server that you're not ready

lock
Locks the amount of players in your team

unlock
Unlocks the amount of players in your team

timeout
Calls a team timeout which lasts for maxTimeout seconds (and it uses up 1 team timeout)

timein
Ends a timeout immediately

cg_enemyHeadModel (default 1)
Set this to "0" if you'd rather not have your "% Frozen" or "% Thawed" indicator drawn when you are frozen.

cg_enemyModel (default 1)
Set this to "0" if you'd rather not have your "% Frozen" or "% Thawed" indicator drawn when you are frozen.

drop <item>*
Drops an item or weapon.

+button5*
Bind this to a key to fire the grappling hook if it's enabled on the server.

g_enablebreath (default 1)*
Set to "0" to disable the breathe effect coming off players.

vsay <command>*
Voice communication. This will send a voicechat message to every player in the game. Replace <command> with any of the following commands:

yes - says "Roger" or "Affirmative"
no - says "Negative"
praise - says "Thanks for the thaw" or "Thank you"
onfollow - says "I'm Following"
help - says "I'm frozen" or "Someone unfreeze me"
helping - says "I'm coming to help" or "I'm on my way"

vsay_team <command>*
Same as vsay but vsay_team only sends the voicechat message to members of your team.

vosay <command>*
Same as vsay but this won't display the text message that comes along with the voicechat message.

vosay_team <command>*
Same as vsay_team but this won't display the text message that comes along with the voicechat message.

cg_teamchatsonly (default 0)*
Setting this to "1" will filter out any non-teamchat message.

cg_novoicechats (default 0)*
Setting this to "1" will filter out all voicechat messages.

cg_novoicetexts (default 0)*
Setting this to "1" will filter out all text messages that come with voicechats. The voicechat will still be played.

cg_noVoiceChatSounds (default 0)
Set this to "1" if you don't want to hear voice chats.

Referee Commands:

ref <password>
Login (authenticate) as referee. Replace <password> with the set ref_password. All ref_ commands can now be used by the authenticated referee.

unref
Un-authenticates a referee. After using this command the referee is no longer a referee and thus cannot use any of the ref_ commands anymore.

ref_clients
Returns a list of players with their client numbers and IP adresses to the referee.

ref_kick <clientnum>
Kicks a player from the server. Replace <clientnum> with the client number of the player that should be kicked. (See ref_clients.)

ref_remove <clientnum>
Removes a player from a team and makes him/her a spectator. Replace <clientnum> with the client number of the player that should be removed. (See ref_clients.)

ref_ban <clientnum>
Kicks a player from the server and adds the player's IP address to the ban list. (See ref_addip.) Replace <clientnum> with the client number of the player that should be kicked. (See ref_clients.)

ref_lock
Locks both teams

ref_lockblue
Locks the blue team

ref_lockred
Locks the red team

ref_unlock
Unlocks both teams

ref_unlockblue
Unlocks the blue team

ref_unlockred
Unlocks the red team

ref_allready
Forces all players to ready

ref_allnotready
Forces all players to un-ready

ref_timeout
Calls a referee timeout, which lasts until the referee disconnects or calls ref_timein

ref_timein
Ends a referee timeout

ref_map <mapname>
Loads a new map. Replace <mapname> with the name of the map to load. Has the same effect as the map command, but this can be called by a referee without rcon or having to call a vote.

ref_restart
Restarts the map. Has the same effect as the map_restart command, but this can be called by a referee without rcon or having to call a vote.

ref_addip <ip>
Adds a player to the ban list. Players on the ban list can not connect to the server anymore. Replace <ip> with the IP adress of the player that should be banned. Use ref_clients to find the player's IP adress.

ref_removeip <ip>
Removes a player from the ban list. Replace <ip> with the IP adress of the player that should be unbanned. Use ref_listip to see the list of banned IP addresses.

ref_listip
Returns a list of IP adresses that are banned from the server to the referee.