I use:
//server name and motd
set sv_hostname "^1Darkmatter" //hostname - visible in server browser
set g_motd "^7Visit our website at ^1http://www.darkmattertrem.freehostia.com" //message of the day - visible while connecting
//passwords
set rconPassword "xxxxxxxxxxxxxxx" //RemoteConsole password - leave blank to disable for more security
set sv_privatePassword "" //password used to take private slot
set g_needpass "0" //if the password below is needed to connect to server
set g_password "" //general password for incoming players
//number of players
set sv_maxclients "24" //total number of clients (normal + private + hidden slots)
set sv_privateClients "4" //private slots count
set g_hiddenClients "0" //hidden clients count
set g_maxGameClients "0" //maximum number of players in each time
//sd and timelimit
set g_suddenDeathTime "45" //if SD mode should be enabled
set g_suddenDeathMode "1" //time for SD mode to kick in
set timelimit "60" //timelimit for map
//connection
set sv_pure "0"
set pmove_fixed "0"
set sv_minRate "10000"
set sv_maxRate "25000"
set sv_minPing "0"
set sv_maxPing "0"
set sv_dequeuePeriod "500"
set sv_minSnaps "20"
set sv_lanForceRate "0"
set sv_timeout "45"
set sv_showloss "1"
set sv_zombietime "1"
//lag correction
set g_unlagged "0" //infamous unlagged
set sv_antilag "0" //imfamous antilag
set g_skipCorrection "1"
set g_maxWarp "3"
//joining
set g_teamAutoJoin "0" //if players will be automatically assigned to teams
set g_teamForceBalance "1" //if teams will be forcibly balanced (maximum 1 player difference)
set g_teamImbalanceWarnings "30" //seconds how often team balance message will appear
//voting
set g_allowVote "1" //if voting is allowed at all
set g_voteLimit "2" //vote limit per player
set g_allowSpecVoting "1" //if spectators can call and vote
set g_suddenDeathVotePercent "75" //percentage of 'yes' votes needed to enable SD mode
set g_mapVotePercent "75" //percentage of 'yes' votes needed to cycle the map
//friendly fire
set g_friendlyFire "1" //friendly fire
set g_friendlyFireAliens "1" //friendly fire for aliens
set g_friendlyFireHumans "1" //friendly fire for humans
set g_friendlyBuildableFire "1" //friendly fire for buildings
set g_friendlyFireMovementAttacks "0" //friendly fire with tyrant trample and dragoon pounce
set g_dretchPunt "1" //dretch punt (no friendly fire for dretches)
//warmup
set g_doWarmup "1" //if warmup will be enabled
set g_warmup "30" //warmup time
set g_warmupMessage "^7Game starts in: " //warmup message
//autodownload
set sv_allowDownload "0" //allow download from server
set sv_wwwDownload "0" //allow download via http (curl)
set sv_wwwBaseUrl "" //URL with maps accessible via http
//g_admin
set g_admin "admin.dat" //admin and ban definition file
set g_adminLog "admin.log" //admin actions log
set g_adminParseSay "1" //if admin commands can be executed from messagemode
set g_adminNameProtect "1" //protect admin names
set g_adminTempBan "5" //automatic ban time after kick
set g_adminSayFilter "1" //if command executed in messagemode should not give 'say' output
//map rotation
set g_mapConfigs "mapconfigs" //folder name with per-map config
set g_initialMapRotation "rotation1" //initial rotation of maps in file maprotation.cfg
//messaging
set g_privateMessages "1" //if private messages should be enabled
set g_publicSayadmins "1" //if non-admin can use /a mode to send message to admins
set g_specsSeeTeamchat "1" //if spectators should see teamchat
//devmap
set g_devmapNoGod "0" //if there should not be /god, /noclip and /give health in devmap mode
set g_devmapNoStructDmg "0" //if buildings should be undestructable in devmap mode
set g_devmapKillerHP "1" //if killer hitpoints should be shown to killed player in devmap mode
//unnamed player
set g_newbieNumbering "1" //if the UnnamedPlayers should be renamed at connect
set g_newbieNamePrefix "^1NewPlayer^7#" //prefix to which UnnamedPlayer is renamed + counter at the end
//minimum levels
set g_minLevelToJoinTeam "0" //minimum admin level to be able to join either team
set g_minLevelToSpecMM1 "0" //minimum admin level to speak in messagemode as spectator
//actions
set g_allowActions "1" //if actions - /me - should be enabled
set g_actionPrefix "***" //prefix before action text
//flood prevention
set g_floodMinTime "2000"
set g_floodMaxDemerits "5000"
//miscellaneous
set g_allowShare "1" //if share should be enabled
set g_maxNameChanges "5" //minutes that must pass to allow player change name again
set g_deconDead "0" //if ready-to-explode buildings should be deconable
set g_lockTeamsAtStart "0" //if teams should be locked at start
set g_clientUpgradeNotice "1" //if players with no GUID should be reminded of obtaining new client version
set g_retribution "1" //if teamkillers should pay back their victims
set g_antiSpawnBlock "150" //If set to '1' it will kill blocker; '0' it will do nothing; '150' it will kick/poke out of spawn.
set g_myStats "1" //if /mystats command should be enabled
//launch initial map
map atcs //start initial map
But you should just add commands you want, or you could just customize the ones above that I use.
