The Linux situation is pretty dire. The developers of (G)ZDoom don't really care about Linux too much and support is often broken. There are patches available as mentioned in the first post but sometimes I've had to go in and edit a snip-it of code myself to get things to compile again. Things like that make me miss binary releases.
I did hear something about ZDoom possibly moving from FMod to OpenAL which would cause GZDoom to follow suite.
Oh and the situation with WADs being (G)ZDoom spefic isn't really an issue as a good majority of the community use the engine.
ps. You might want to check out Skulltag, which provides online play (DM,CTF,Coop,etc) and is based off of GZDoom. The community there is surprisingly active and there's plenty of players and servers at any given time. It is closed source however but that just means you don't have deal with compiling. >_>