Is there a particular application/format combination that would eliminate those little pauses between threaded tracks on audio CDs? Or a player that cleans them up at all?
What are you using for ripping atm? What do you mean pauses between tracks? I take it your current ripping program places a small extra gap, so when it encounters a track that isn't supposed to have one it inserts one anyway? I use CDeX for my CD ripping, and it's a great program. Perfect rips every time.
pauses shouldn't be added by any decent ripper worth its salt. i use and recommend dbpoweramp; but it's very much a tidal wave of functionality presented in a not particularly user friendly way. it's great if you have very specific music ripping needs (i have it configured to rip simultaneously to FLAC and MP3 into separate libraries), otherwise it's probably slight overkill.
I think it is generally the playback software that introduces the small gaps between tracks. See here for details: http://en.wikipedia.org/wiki/Gapless_playback I think Foobar (and some other playback software) support gapless playback of correctly tagged MP3s. Also, EAC really is the bollocks for accurate rips, and has all the features you could ever need