Converting FLAC into Apple Lossless [in Windows]
I found a great little script that seems to do the job:

iTunes Automation: Convert FLAC Audio Files to Apple Lossless

Although there's a tiny bug at present (v0.91) meaning it will only convert one file at a time. To fix it, just change line 275 from

fso.DeleteFile(tempWAVPath)


To

fso.DeleteFile(tempWAVPath, true)


And you're set.