I've decided I'm going to re-rip and encode (the good) parts of my CD collection to a lossless format, I guess that means FLAC or APE, any advice guys?

Well, what's important to you?

Personally, I'd just stick with FLAC. I don't think the pros of APE (by which I mean the slightly better compression ratio) are sufficient to justify using it, given its cons.

Nothing plays APE. FLAC or ALAC (or WAV or AIFF uncompressed) are your only (realistic) options if you want to play the files without first converting.

You should probably evaluate what your management/handling/playback ecosystem looks like before deciding. Though it should be straight forward to batch-convert between formats at a later time if you need to.

One more thing... The table/wiki linked above contains a number of inconsistencies and out-of-date information. ALAC and FLAC have decent hardware support. At least any hardware product that matters supports one or the other or both.

FTFY.

"that matters" = commercially available retail product. Not exactly a generalization, and therefore, probably doesn't count for full points on the true Scotsman retort.

Bottom line: APE = obscure, FLAC and ALAC = much more widely supported.

So this begs the question: what is the advantage of APE? Does it claim better compression ratios or something?

Personally, I initially ripped all my CDs to FLAC. I then converted all of those to high bitrate MP3s, because MP3 is just easier to use in more places and on more hardware. The FLAC files were moved to a spare hard drive as a digital locker of sorts.

After hours and hours of work to do all this, I have never once gone back to those FLAC files, and I'm now using Google Music and rdio to play all my music anyway...

Yes, I would say the only true advantage is the slightly better compression. In the days of 4TB hard drives I would say this really is a non issue. Take a single CD, call it 800MB. Based on that sample set:

FLAC -> 469.7MB
APE -> 444MB

25MB difference per CD is nothing...

APE has less support compared to FLAC so it's a no brainer to me. I haven't done this myself after ripping all my old stuff to MP3 a long time ago. I now rip to FLAC always.

The only FLAC con is listed as "no bybrid/lossy" mode. USing that would kind of defeat the purpose of using FLAC so that's a non issue.

I didn't see a "gapless" feature. I know FLAC is but I presume APE is also since it's reconstructing the original sample data 100% intact.

What I'm thinking is that I'll just re-rip the stuff that I listen to a lot and encode it losslessly for playback at home (Squeezebox or MediaMonkey) while leaving in place the original MP3s for the iPod. The only problem is that since the demise of allmusic there isn't a place to d/load high bitrate audio, some stuff on Amazon is 128 and they don't even tell you what the bitrate is before you buy.

I also seem to have mould on my CDs, just started ripping yesterday and a lot of the disks have patches of what looks like white mould on the playable side. It wipes off OK and no errors during ripping but wasn't expecting that, especially since the inserts are dry and non mouldy. The last time I played any of them must have been at least 8 yrs ago.