I really only keep MP3 files, I have flacs as well, but usually convert them to mp3. In my humble opinion there’s only one tagger you should use on Linux, EasyTAG.
I love the layout and the amount of tags you can edit but if you ask me which tagger is the best I would answer Tag&Rename.
The fact you can download album info from Amazon.(com|co.uk|de|co.jp|ca) makes this tagger. I haven’t stumbled up on an album yet which gave me the wrong information using the Amazon lookup. Let me clarify that, yes I have had lists of possibilties for one album and some of them were incorrect but their always has been a correct one as well. Recently I found an album that I couldn’t find on Amazon.com and it turned out it was a UK release and amazon.co.uk gave me the right info. The other very good part is the album cover download through Amazon. Unfortunately this only runs on Windows and I don’t won’t to run it under Wine.
Hopefully the people at Tag&Rename will create a Linux port, I sure hope so.