Hi guys - just found this forum looking for gen on the DSP3100's but couldn't help see your thread and want to contribute hope your still watching for posts :-)
I use EAC via iTunesencode.exe into iTunes - so I get WAV's with full tag info, although this is stored in the iTunes database not the files themselves. Have been thinking of going over to AIFF - so the tags can be in the files and I can drag album art into iTunes (not possible with WAV) - have listened to FLAC and I can hear a difference via my Squeezbox 3 (the decoding isn't wrongly implemeted or anything, I just think the SB in-built FLAC decoding generates more digital noise than the pure WAV sent over from the PC and it might be interfering in the analogue domain - but might just have had a 'golden ears' night and too much vino :-)
Haven't heard the Sonus little baby, but love the remote - Squeezebox I can confirm is stunning transport and has displaced my 508/24. I run it into a 566/24, 502 pre and 507 power amp. Speakers are weak link at moment (hence looking to cut out all the electronics and feed SB3 straight into DSP3100's!) although Ruark Prologue 1's suited my room better than the Sonus Fabers I had when I moved (way too much bass!)
EAC is a pain to set-up right but worth it in the end - at least I know I have bit perfect file and bit perfect playback right into the SB3 :-)