Is it possible to run multiple mods at a time? Reason I'm asking is I know one of the mod's I run there is no source code for it, so really can't alter it, but I'm thinking it would be nice to add a few administration plugins to it. Including Mysql logging of events.
Not really. You could disassemble the byte code and patch in more functionality but that's so complicated you'd only do it if your life depended on it.
So the only way it would be possible is to edit the actual server binary (edit the source code for quake/ioquake) to load additional libraries, to accomplish what I'm looking for?