When I rip vinyl, I go to WAV at all the bandwidth my DAC can handle (192kHz, 24-bit). Makes a HUGE file for, say, an album. I use some software that guesses where the breaks are based on the track length input and blank space, but it's not very good, and I have to manually adjust every track (a real PITA). I then down-convert the WAV files to Apple lossless. I adjust the sampling rate down to 48kHz, because that's as much as my Squeezeboxes can take, but I keep the WAV files to play direct through my big rig off the attached computer. I do the same with SACDs through the Oppo.
For ripping directly from CD (or hybrid SACD), I use Apple lossless directly into iTunes. The only reason I use that codec is that it's what iTunes uses, and iTunes is directly recognizable by the software that runs my Squeezeboxes (SqueezeCenter). I hear FLAC is good too, if you use Winamp as a player.