Most modern Linux games are now using Simple DirectMedia Layer 2 while ioquake3 is finally preparing to make the official jump to SDL2 from SDL 1.2. The ioquake3 developers are hoping for Linux gamers to test their updated Q3A builds to see how the port to the updated library is panning out. The many games derived from the ioquake3 engine will also need to (ideally) pull in the updated code and release new updates.
The SDL2 transition was announced on Monday at ioquake3.org. Sadly there's nothing new to report at this time on ioDoom3, the open-source engine fork of the more modern id Tech 4 engine.