I have a large music collection that consists mostly of FLAC files and mp3 files that have a variety of tags, (id3v1, id3v2, ape, vorbis) My question is should i convert them all to one or leave them as is? I plan on getting an ipod soon and when transfering the mp3's i dont wanna find out that one is incompatable.

With experience with an iPod. For MP3s use id3 and only use one of them in the file. Having both v1 adn v2 can come up with some problems. Avoid ID3v2.2 I personaly use 2.3.

With FLAC what is the standard tag format? Is it FLAC or OGG? For my FLAC I just use the standard tag format set through the command line

FLAC uses vorbis comments. Personally I wouldn't recommend using id3 tags on flac's, although you can do it. It always seems best to use the tagging format that a an audio codec was designed for.