There are lots of good lossless encoders.
Monkey's Audio has some advantages, like having the highest efficiency of any lossless codec. (space used for a given CPU usage) It also has freely available source that isn't covered by a restrictive, viral license. However, it has some disadvantages, like that stupid monkey picture.
So, take your pick -- you probably won't go too far wrong.
Generally I agree fully...
However, there is currently no APE support for any OS other than Windows. For me this is a dealbreaker -- game, set, match. Also, whether you consider a viral license == restrictive license depends on your point of view. I would view any license that does not explicitly grant me rights to re-use the source to be restrictive. Since any application I would ever write would be given away free and also Open Sourced, I could care less about the Viral "clauses" of the GPL (and if I was concerned, there's plenty of stuff available under both the LGPL and the BSD licenses, which don't have anywhere near the viral implications of the regular GPL). However, if I intended to use the work in a commercial software release, like MC, I might be more wary of them.
As far as the monkey.... I think that's an advantage. But of course, I like monkeys.
[voice=monkey]ooh, ooh, ooh[/voice]
From everything I've read, the most common lossless format out there would be WAV (not WAVPack, just regular old WAV), followed by SHN. Not because they're better (they're not) but because they're older.
For newly encoded media, all I ever see available online (like at Lossless Legs and Etree) is FLAC and SHN files. I've never seen an APE available online for downloading, but that's just me. Of course, as I've said before, my ears can't hear the difference between a FLAC/APE/SHN/or-whatever-the-heck-lossless-format and a "preset extreme" VBR LAME MP3. I just use MP3 for my stuff.