If you buy or download music in FLAC files, you do so because you want the best quality audio files. FLAC files are losslessly compressed, which means that, when you play them back, they are bit-perfect replicas of the original uncompressed files (on a CD or high-resolution files).
You may want to play these files in iTunes. While iTunes doesn’t support FLAC files, it’s very easy to convert them to Apple Lossless, or ALAC, an equivalent lossless format that iTunes does support. Converting audio files from one lossless format to another is lossless; in other words, there is no quality lost when you convert from FLAC to ALAC. (The same is true with other uncompressed or lossless formats, such as WAV, AIFF, APE, SHN, and others.)
The best app for doing this on a Mac is the free XLD. It can convert too and from just about every audio format you will even want to use, and does so retaining metadata; tags with track info and album artwork. It’s quick and easy to use, and you can either keep your original FLAC files, or delete them after conversion and just keep the ALAC files. (You can always convert them back to FLAC later if you want, with no loss in quality.)
If you use Windows, you can get a free version of dBpoweramp, which can convert files, and a paid version, which you can use to rip CDs, edit tags and more.
There used to be some third-party tools that hacked iTunes to let you add FLAC files, but they’re not reliable. If you want to use lossless files with iTunes, it’s much easier to just convert them.
One other useful tool, if you use a Mac, is Rogue Amoeba’s Fission. This audio editor is my tool of choice for trimming, joining, and editing audio files, and it also includes a conversion tool that lets you convert from just about any audio format to AAC, MP3, Apple Lossless, FLAC, AIFF, and WAV. While it’s not the best tool if you only want to convert audio files, it is the easiest-to-use Mac app for editing those files.
One more thing. Don’t convert lossy files to lossless; they don’t sound better. (You’d be surprised how many people write me thinking they will.)