My favorite would have to be the WavPack hybrid lossless. That said, I know that FLAC will probably be the most popular lossless codec for a long time.
I performed tests and found that WavPack, even when in hybrid mode (-b2.0 -c -cc -hh), created a smaller set of lossless files than FLAC (1.2.1 @ 8). APE is still the supreme champ at creating small lossless files, but I foresee fading away as development seems to have stopped. WavPack and FLAC will catch up with it, and will one day surpass it.
Other thoughts: "Since you are going with the non-conventional formats..."
click to show Since you are going with the non-conventional formats, you might as well spring for the full extras package and get
Rehash to hash your files (MD5 and TIGER hashes are popular these days) and propose to users that they should install
HashTab. More info just start skimming this
TFP thread here.
I really suggested HA and FB2K (I edited that out) too soon. I just read your reply to my post in The Open-source/Freeware thread, and I don't have to preach.