Tyrann is being a busy bee on Tyrquake again, adding http://disenchant.net/git/gitweb.cgi/?p=tyrquake;a=shortlog. It looks mostly like bug fixing and code clean up.
http://www.quakeforge.net/ is in serious development as Taniwha http://quake.git.sourceforge.net/git/gitweb.cgi?p=quake/quake;a=shortlog on a GLSL based engine, tools and everything that is not set in stone. Did you know QuakeForge includes some fantastic utilities for PAK and WAD files? Map compilers?
http://mhquake.blogspot.com/ (DirectQ coder) seems to be more excited about Doom 3 and Quake 2 at the moment. Findings from the Quake 2 hacking already went into DirectQ though. I wish he had a public commit log too.
Quakespasm is continually developed but http://sourceforge.net/projects/quakespasm/develop does not seem to have a short log overview so I have no idea what is going on… (No, I cannot be arsed to do a checkout.)
http://fteqw.com/ is not getting any homepage update love but as usual it is in constant, heavy development. A notable recent feature is SQLite support. Someone please backport this to “normal” engine, it would be incredibly insanely fantastically useful.
DrLabman https://github.com/DrLabman/QMB/commits/master. It looks like QMB is going to C++ but maybe it always used that and I just did not know (or care) before. It also runs on Linux.
https://github.com/atphalix/eviltoys. Not sure if it uses Darkplaces or Tyrquake in the end.
http://www.quaddicted.com/_media/engines/engine_blinky_panini.gif
I never got it to compile because of LutJIT weirdness but https://github.com/shaunew/blinky engine looks awesome. Based on Tyrquake it takes http://www.strlen.com/gfxengine/fisheyequake/ to the next level by adding MANY projections.
Whatever libxenon is, https://github.com/lantus/sdlquake-libxenon port uses it.
http://www.quaddicted.com/_media/engines/game_doodle_2.jpg
The creatively named http://www.doodlethegame.com/ (https://github.com/klaussilveira/Doodle) is “a game that aims to provide a fun audiovisual experience instead of innovative gameplay”. It uses NPRQuake for a doodle-ish rendering effect. Sadly it looks abandoned.
And in the comments below you will find the coders correcting my mistakes and publically talking about more of their recent work. 