Ever since its release, Jedi Academy is probably one of the most easily modded (modified) games out there. There are a few sites still hosting many of the mods created:
First, a word on installing the mods. Most mods come as one or more .pk3 files. If you want the changes to appear in every server, you need to put the .pk3 files in your GameData\base folder, usually C:\Program Files\LucasArts\Star Wars Jedi Knight Jedi Academy\GameData\base. Files with alphabetically higher names get higher preference over files with alphabetically lower names, so naming a pk3 file zzzzzmymod.pk3 will ensure it gets loaded first.
For CTF, there are a few mods that every player should consider:
Client mods are modifications to the client-side game (as opposed to the server-side which is usually run on a remote computer). They can improve your gameplay, fix annoyances in the original game, or simply customize your game more to your preference. The two main ones are:
Sil's Client Mod (SMod)
Get the latest one at https://sites.google.com/site/silsjka/, which also has a full description of all tweaks. This is the most popular CTF clientmod in use. Attached at the bottom is a mirror of the latest versions at the time of writing.
Teh's Client Mod
This client mod is a lighter mod than Sil's, offering only small but useful tweaks over the vanilla game. Many of the changes were integrated into Sil's mod. The latest version is attached at the bottom of the page - make sure to also download curl_dep.zip and extract it into your GameData folder. Some notable changes:
new compact scoreboard, includes spectators at the bottom
team-based forcemodel - lets you set all players on your team to one model and all players on the enemy team to a different model. cvars:
\cg_forceModel 1 - force all players to be your model
\cg_forceTeamModel 1 - enable the team-based forcemodel
\cg_friendModel "stormtrooper" - specify which model to use for allies
\cg_enemyModel "reelo" - specify which model to use for enemies
semi-transparent console background lets you see the game behind the console
changed force sight shader to make players more visible when using sight
decreased the opacity of fullscreen tints (when using force protect, force absorb, or rage) in first person (by 4x), making it easier to see while using them
add flag-drop icons that display when flags are dropped and not yet returned - disable with \cg_drawFlagDrop 0
add countdown timers for force boon and dropped flags to indicate when they will be respawned - disable with \cg_drawRespawnTimer 0
auto-download of maps if you don't have them.
enable with \cl_wwwDownload 1
specify a default website to download maps from with \cl_wwwBaseUrl "http://baseurl.com" - the pk3 name will be appended to this if the server doesn't specify a server-specific site
if the map can't be downloaded for any reason, instead of dropping the game will attempt to connect using the ffa1 map instead. often times you will error out, but it may provide enough time to vote the server to a different map that you do have.
automatic recording of demo file for every game. at the end of the game, the demo will be deleted unless you run the command \niceshot in your console (or use a bind). if you do use the command, at the end of the game, the file will be renamed to the times at which you pressed the bind.
disable the feature by using \cg_noAutoDemo 1
the command \cg_fixDemoScores 1 will send a request for the current scores to the server every 2 seconds. without this, it will only be possible to view scores when watching a demo when the player had originally watched the scoreboard. with it enabled, the scores will be updated every 2 seconds while watching.
disable the JA+ message of the day printspam on each map load by using \cg_disableJPMOTD 1
draw the player's current speed below the game FPS with \cg_drawSpeed 1, and the current acceleration with \cg_drawAccel 1
Unfortunately the popular JA+ mod isn't very useful for CTF. Its features are aimed toward making saber enhancements, and making servers where the majority of time is spent sitting around while a small number of players duel. The mod itself has not been updated in a very long time. Regardless, for completeness, you can download the last version from http://www.gamefront.com/files/21104289/JA__Mod_V2_4_Build_7_.
Red Slushie Flags
Red Slushie was a mod made by stubert (rise-dan) in the early years of JKA. One of the enduring features that's been extracted into an independent mod is the tweak to the flags - it changes them to be semi-transparent, letting you see through them in third person when they're on your back. Find the pk3 attached at the bottom of the page.
Recently, Raven released the entire source to the game, including the game engine. As a result, it's now possible to modify the engine as well (jamp.exe). Included at the bottom is a build containing fixes for the most crippling bugs in the original engine (notably, it's now possible to start a game locally while in widescreen mode without crashing). For a far more ambitious engine mod, try the OpenJK project.
Custom maps help keep the game fresh, since by default the game comes with just 5 capture the flag maps. Many maps have been created for the game. Some of the most popular ones are collected in this google drive folder: