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When doing anything lossless, I almost ALWAYS run for FLAC - even though Monkey's Audio sometimes gets better compression for me, FLAC has the best support (both hardware and software) and it's open source to boot (I always make an effort to use open source software when I can). Whenever I get a vinyl, I immediately rip it, encode to FLAC, then archive it on CD - there's nothing worse than finding out the track you've been building up for for hours has a big 'ol scratch in it Whenever I'm done with a track, I encode the 24-bit/96khz wave track pre and post master to a FLAC file and archive it too. Just in case 
Other than FLAC and Monkey's Audio, there is also Apple Lossless - which is being made more popular by iTunes and the iPod, but it doesn't really offer much in terms of usability - and Shorten, which you'll see often used for encoding concert performances over at the Live Music Archive at Archive.org (free Dave Matthews concerts? yes please).
In my personal use though, FLAC is my lossless codec of choice. Multiple OS/software/hardware support, streamability, good compression ratios, and open source do it for me.
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