Hi Brent!
I use 48kHz all the time. admittedly, I don't do speech communication with
jack (voip and co.). But I have never yet experienced problems with
LinuxSampler, mplayer, my DAW. Even the old beatrix could work with 48kHz.
Fluidsynth and ZynAddSubFX need an option - at least on the commandline -, but
they do the trick.
I would know about using 96kHz as a standard, since I never had reason to,
save for one or two experiments.
Warmly yours
Julien
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http://juliencoder.de/nama/music.html