Based off of Quake2CTR v1.0.  I take very little credit for these, I simply compiled what MasterFeizz and MrHuu put together.  I recommend using the .cia builds.  When testing the .3dsx builds on my O3DS, the BFG and weapons from the mission packs were missing their skins unless I dropped the texture quality.

CTR: Vanilla Quake 2.
ACE: ACEbots for multiplayer.
CTF: Capture The Flag multiplayer mode.  https://www.doomworld.com/idgames/idstuff/quake2/ctf/q2ctf150
CTC: Catch the Chicken.  Multiplayer fun.  https://www.moddb.com/mods/catch-the-chicken
DDAY: D-Day: Normandy mod.  A World War 2 themed, MP-focused total conversion.  http://www.ddaydev.com/site/index.php
XATRIX: Mission pack 1, The Reckoning.
ROGUE: Mission pack 2, Ground Zero.
ZAERO: An unofficial mission pack, Zaero.  https://www.moddb.com/mods/zaero

Credits:
MasterFeizz - Initial port
MrHuu - Porting mods and mission packs
EvilJagaGenius (me) - Compiling

Enjoy!
-Jaga