Somebody sent me an email asking about this, but my response got so damn long, I thought I might as well post it publicly so other people don't have to ask.
Hey, what is the difference between FLAC and Windows Media Lossless?? Which is better?
Well, since they're both truly lossless formats, you're capable of converting to the exact same WAV/AIFF/RAW file from either of them, and during playback they should sound the exact same as each other. What makes one lossless format different from another is never the quality, but always the utility. FLAC is widely considered to be more useful than WMA-Lossless because it decodes/playbacks so much smoother when you're doing anything other than realtime, like jumping to a specific point within the song, or converting to some other type of file.
WMA-Lossless files are faster to create, but slower to use. The old FLAC argument is that you encode your lossless file only once, but you decode/playback it many times, so if you can take longer to create a faster-loading file, then the extra time 'spent' early on is actually 'saved' over the long run. I know that sounds counter-intuitive in a world where different compression levels of ZIP or RAR will extract faster if they took less time to make, but audio-specialized compression is very different in that WMA-Lossless or Apple Lossless cut some corners to get a file as small FLAC but in less time. FLAC will take longer to compress because it's creating separate chunks within itself, for each of the different split seconds throughout the entire song. Apple Lossless and WMA-Lossless work with larger chunks, which means you can't hear Point M within a song, without the player also having to quietly load Points L and N first, and that creates noticable delays. Monkey's Audio (another lossless format) is the biggest abuser of this sort of thing, and it squeezes an overall song even further... in the same amount of time, and your ability to convert the song or seek to a specific point within it, are terrible, and arguably not worth the extra 'savings' on storage space.
WavPack (my lossless format of choice) tries to be the best of both worlds, between the decoding speed of FLAC, versus the smaller filesize of Monkey's Audio. It doesn't really beat them both, but I'd say it's a silver medalist in both fields, which arguably makes WavPack a more.... balanced format. WavPack is also the king of 96kHz/24bit, in that no other lossless format has as much Compression Size versus Decoding Speed efficiency for audio of that scale, while other lossless formats unofficially specialize in 44.1kHz/16bit even if they allow 96kHz/24bit.
The thing that's so important about decoding speed (aside from what I mentioned so far), is it affects battery life on portable players. If a format is 'faster'/'smoother', that means on the flipside, it is taking less processing for normal playback. Less processing ends up costing you less power. Lossless formats in general, are energy hogs on portable players, but FLAC is "the lesser of many evils". But no matter which one you use, it's supposed to be effectively the same as having a portable CD player, only it's more compact and more convenient.
The other downside to WMA-Lossless is that it is commonly associated with Digital Rights Management (DRM). That is to say, songs you have ripped or bought, are exclusively locked to a specific computer or a specific player. It doesn't have to be that way - you potentially can create WMA-Lossless files that function on other computers or players without any bullshit, but when you're using convenience tools from Microsoft to perform the rip, they rarely or never give you that privilege. When you have to "Synchonize" songs to your player, there is almost always some degree of DRM going on, and even if you don't have to use a special interface, but can do your own drag & drop or copy & paste, if your portable player shows up in My Computer as anything other than a drive letter (E, F, etc), then Windows is quietly implementing DRM in the background, and that's what "Plays for Sure" is all about. This problem isn't exclusive to WMA-Lossless though - Microsoft has ways of quietly encrypting any format they 'support', including MP3, and this happens on nearly any non-iPod player you can buy at retail stores nowadays - not just Zunes. WMA-Lossless is a commonly DRMed format not because it was specifically designed to be, but because Microsoft loves DRM in general, and in most cases where you'd ever be using WMA-Lossless, you're using Microsoft tools and playing by Microsoft's rules.
The common dilemma with WMA-Lossless is that depending upon your situation, you might end up feeling the same way about it, that some people do about the opposite gender - can't live with it, and can't live without it. FLAC being a better format, is mostly irrelevant if you're stuck using whichever player(s) Apple or Microsoft wants you to use. The best damage control is to make informed decisions from the very foundation, and base your choice of player on the format, rather than base your choice of format on the player. You can live outside of those two corporate spheres of format influence if you use a software player like foobar2000, and a portable player from a company like iAUDIO (or a Rockboxed iPod) - and it's truly liberating, rather than simply trading one brand of bullshit for another. There's also cog for OSX, though I'm not sure that it supports APE tags.
If you should ever decide to try out noncorporate lossless formats, you might be bewildered to stumble upon different compression levels
. FLAC has 9 levels that compared to each other, work much like the different degrees of ZIP/RAR compression & decompression. WavPack also has different settings, but instead of numbers, they have names like "Fast", "Normal", "High", etc.. Monkey's Audio also has different compression amounts, and it's highest option is called "Insane", pretty much because you'd have to be insane (in a misinformed way - not a taking things overly seriously kind of way) to actually use it. The problem with Monkey's Audio is that if you're not using Insane for the extra space savings, then there's really no point in using it (in-place of other lossless formats) at all, so that's practically the only Monkey's Audio option that people ever choose, and most folks don't understand the decoding price they pay on the storage 'savings'.
In the end, the 'better' lossless format really depends upon how you intend to use it, since they're each oriented in different ways.
P.S. Even if you choose the right format, it still doesn't necesssarily mean you're ripping CDs properly (I'd tell you to Google around for "Offset Correction" - but the ideal tutorial for it is now gone). Lossless perfectly preserves whatever you feed into it - which most of the time is imperfect to begin with. CDs may be digital, and people think digital copying is automatically perfect, but Audio CDs in particular, have a sloppy standard that introduces little-known inconsistencies on ripping and burning, even on brand new flawless-looking discs. If your CD/DVD drive misperceives any part of an album, this gets passed onto whichever lossless format you're using.
There's the additional Murphy Law that "Everything is always in the last place you look", but I extend that thought into "People will stop looking for something after they think they've already found it". Just keep in mind that lossless audio compression alone, isn't the complete situation of perfect CD ripping. I'll post more about Offset Correction later. Someday I'd like to put together a list of raw CRC/MD5 checksums you get when you rip a Ringo/Jihen CD with a proper setup, so you'll know whether or not your calibration was right.