Tagging is more of a problem than filenames, because vorbis comments, which is what FLAC uses, aren't particularly standardized.
For instance, while there is TRACKNUMBER for the number for the track, there is no set tag to express the total number of tracks and different programs do different things.
The tagging for classical music could get cocked up quite spectacularly on transcoding. You can use COMPOSER for MP3 and MP4/AAC files (and iTunes, for example, will display that). The vorbis comments, however, expect the composer's name to go in the ARTIST field and the orchestra, conductor, etc. to go in the PERFORMER field.
This kind of thing can cause problems with tags not carrying over from one format to another--for example, see
here.
The Hydrogen Audio site has a page in the wiki entitled
Foobar2000:Encouraged Tag Standards.