well you could create a file called autoexec.cfg containing all your main stuff like
// ----------------------------
unbindall
// Player info
set cl_run "1"
set cg_autoswitch "0"
set cg_fov "105"
set cg_zoomfov "65"
set handicap "100"
// Controller settings (mouse)
set in_joystick "0"
set in_mouse "1"
set cl_freelook "1"
set sensitivity "5"
set cl_mouseaccel "0"
set m_pitch "0.022"
set m_yaw "0.022"
set m_filter "1"
bind MWHEELDOWN "weapnext"
bind MWHEELUP "weapprev"
bind MOUSE1 "+attack"
bind MOUSE2 "+moveup"
bind MOUSE3 "weapnext"
// rcon shit
// Sound
set s_khz "22"
set s_compression "0"
set s_mixahead "0.2"
set s_mixPreStep "0.05"
set s_doppler "0"
set s_separation "0.5"
set s_volume "1"
set s_musicvolume "0"
// Connection settings
set cg_nopredict "0" // 0
set cg_predictItems "0" // 1
set cg_smoothClients "1" // 0
set cl_allowDownload "0" // 0
set cl_maxpackets "63" // 30
set cl_nodelta "0" // 0
set cl_packetdup "1" // 1
set cl_timeNudge "0" // 0
set g_synchronousclients "0"
set rate "12000"
set snaps "40"
// Server browser
set cl_maxPing "550" // 800
set ui_browserGameType "0" // 0
set ui_browserMaster "3" // 0
set ui_browserShowEmpty "1" // 1
set ui_browserShowFull "1" // 1
set ui_browserSortKey "3" // 4
// System Setup - Display
set cg_viewsize "100" // 100
// Setup - Game options
set cg_simpleItems "1" // 0
set cg_marks "1" // 1
set cg_brassTime "0" // 2500
set r_dynamiclight "1" // 1
set r_fastsky "0" // 0
set r_finish "0" // 0
set cg_forceModel "1" // 0
set scr_conspeed "9999" // 3
// Models/Skins
set headmodel "crash/pm" // sarge
set model "crash/pm" // sarge
set team_headmodel "crash/pm" // *james
set team_model "crash/pm" // james
// Additional settings
set cg_gunsmoke "0" // 1
set cg_gunX "0" // 0
set cg_gunY "0" // 0
set cg_gunZ "0" // 0
set cg_noprojectiletrail "1" // 0
set cg_deferPlayers "1" // 1
set cg_drawFriend "1" // 1
set cg_gibs "0" // 1
set cg_scorePlums "1" // 1
set cg_shadows "1" // 1
set cg_thirdPerson "0" // 0
set com_blood "1" // 1
set com_maxfps "125" // 85
set r_swapInterval "0"
set r_textureMode "GL_LINEAR_MIPMAP_NEAREST"
set r_finish "0"
set r_dlightBacks "1"
set r_dynamiclight "1"
set r_drawSun "0"
set r_fastsky "0"
set r_ignoreGLErrors "1"
set r_stereoSeparation "64"
set r_zproj "64"
set r_flares "1"
set r_lodbias "-1"
set r_lodCurveError "250"
set r_greyscale "0"
set r_ignoreFastPath "1"
set r_stereoEnabled "0"
set r_smp "0"
set r_subdivisions "4"
set r_simpleMipMaps "1"
set r_customPixelAspect "1"
set r_customheight "1024"
set r_customwidth "1600"
set r_ignorehwgamma "0"
set r_overBrightBits "1"
set r_depthbits "0"
set r_stencilbits "0"
set r_colorbits "0"
set r_texturebits "16"
set r_detailtextures "0"
set r_picmip "0"
set r_ext_max_anisotropy "2"
set r_ext_texture_filter_anisotropic "0"
set r_ext_texture_env_add "1"
set r_ext_compiled_vertex_array "1"
set r_ext_multitexture "1"
set r_ext_compressed_textures "0"
set r_allowExtensions "1"
set r_roundImagesDown "1"
set r_mode "4"
set r_fullscreen "1"
set r_glDriver "opengl32"
// Weapon settings
set color1 "6" // 4
set color2 "9" // 5
set cg_oldPlasma "1" // 1
set cg_oldRail "1" // 1
set cg_oldRocket "1" // 1
set cg_railTrailTime "1125" // 400
set r_railCoreWidth "4" // 6
set r_railSegmentLength "61" // 32
set r_railWidth "4" // 16
// HUD
set cg_bobpitch "0" // 0.002
set cg_bobroll "0" // 0.002
set cg_bobup "0" // 0.005
set cg_crosshairX "0" // 0
set cg_crosshairY "0" // 0
set cg_crosshairHealth "0" // 1
set cg_crosshairSize "24" // 24
set cg_draw2D "1" // 1
set cg_draw3dIcons "0" // 1
set cg_drawAmmoWarning "0" // 1
set cg_drawAttacker "1" // 1
set cg_drawCrosshair "1" // 4
set cg_drawCrosshairNames "1" // 1
set cg_drawFPS "1" // 0
set cg_drawGun "0" // 1
set cg_drawIcons "1" // 1
set cg_drawRewards "1" // 1
set cg_drawStatus "1" // 1
set cg_drawTeamOverlay "1" // 0
set cg_drawTimer "1" // 0
set cg_lagometer "1" // 1
set cg_runpitch "0" // 0.002
set cg_runroll "0" // 0.005
set cg_teamChatHeight "4" // 0
set cg_teamChatsOnly "0" // 0
set cg_teamChatTime "3000" // 3000
set cg_smoothClients "1"
set r_subdivisions "4"
set r_customwidth "1600"
set r_customheight "1024"
set r_customPixelAspect "1"
// --------
// CONTROLS
// --------
// Movement
bind a "+moveleft"
bind c "+movedown"
bind d "+moveright"
bind f "+button2"
bind r "say thank_you"
bind s "+back"
bind u "kill"
bind v "say_team help! they got me

"
bind w "+forward"
// Mouse
bind MOUSE1 "+attack"
bind MOUSE2 "+moveup"
// Menu
bind TAB "+scores"
bind ESCAPE "togglemenu"
bind [ "weapprev"
bind ] "weapnext"
// Join, vote, ready
bind F1 "vote yes"
bind F2 "vote no"
bind PGUP "ready"
bind PGDN "notready"
// Communication
bind t "messagemode" //chat all
bind y "messagemode2" //chat team
// HUD font settings (requires cg_enableOSPHUD set to 1)
set cf_AmmoStatusbar "8x8" // 8x8
set cf_CrosshairNames "12x12" // 12x12
set cf_Following "8x12" // 24x24
set cg_teamChatHeight "5" // 0
set cg_teamChatTime "60000" // 3000
set cf_Fragmsg "8x8" // 16x16
set cf_Pickupstring "10x14" // 10x14
set cf_Scores "16x16" // 16x16
set cf_Statusbar "32x32" // 32x32
set cf_Teamchat "8x11" // 8x12
set cf_TeamCrosshairHealth "12x12" // 12x12
set cf_Teamoverlay "9x10" // 6x11
set cf_Vote "8x8" // 10x14
set cf_WeaponName "12x12" // 12x12
set cf_WeaponSwitch "32x32" // 32x32
// General game options - HUD - general
set cg_crosshairHealth "0" // 1
set cg_crosshairPulse "1" // 1
set cg_Customloc "1" // 0
set cg_damageDraw "0" // 1
set cg_damageKick "0" // 1
set cg_drawCrosshairNames "2" // 1
set cg_drawGun "0" // 1
set cg_enableOSPHUD "1" // 1
set cg_fallKick "0" // 1
set cg_float "0" // 0
set cg_lagometer "1" // 1
set cg_MaxlocationWidth "16" // 16
set cg_muzzleFlash "1" // 1
set cg_nochatbeep "0" // 0
set cg_NoMOTDDisplayDuringDemo "0" // 0
set cg_q3compScoreboard "1" // 1
set cg_scoreTransparency "0.6" // 1.0
set cg_statscrolltime "0.15" // 0.15
// HUD (requires cg_enableOSPHUD set to 1)
set ch_3waveFont "0" // 0
set ch_ColorLocations "1" // 1
set ch_CrosshairColor "7" // White
set ch_CrosshairNamesLeft "0" // 0
set ch_crosshairTeamInfo "1" // 1
set ch_drawFlagNames "2" // 2
set ch_drawHealthMeters "0" // 0
set ch_drawPickup "1" // 1
set ch_drawSpeed "0" // 0
set ch_FilterLocationsTeamchat "0" // 0
set ch_fragMessage "1" // 1
set ch_graphs "1" // 1
set ch_InverseTeamChat "0" // 1
set ch_Obituaries "1" // 1
set ch_Pickupitem "1" // 1
set ch_StatusbarFormat "10" // 10
set ch_statusbarStyle "1" // 1
set ch_TeamBackground "0" // 0
set ch_TeamchatOnly "1" // 0
set ch_TeamCrosshairHealth "1" // 1
set ch_Teamoverlay "p12n h/aw l" // p12n h/aw l
set ch_weaponList "1" // 1
set ch_weaponListBackground "1" // 1
set ch_weaponListDrawAll "0" // 0
set ch_weaponListFlash "1" // 1
set ch_Weaponswitch "6" // 4
You can usually put everything in this file (as well as scripts so you can have /exec anyname.cfg rather than tons of commands).
Since these commands use 'set' they dont get written permantly (use seta for that) but they are set each time you launch the game. This means you can be sure things are set the way you want and you wont get any file too big errors.