I have a copy of each song in .ogg and .flac in each album folder.
Is there anyway to keep Winamp from automatically playing the .ogg version because it will play the song twice, first flac then ogg. I tried removing .ogg from File Types but that didnt work. Any ideas?

You can disable the ".ogg" support in Winamp by removing (renaming) the plugin in_vorbis.dll, located in "plugins" directory. For example, you could change the extention to ".dll.off" so if you need the ogg support in the future, you should just remove the last extention.

you mean some kind of filter for the winamp playlist? hmm. interesting one there.

you'll have to look for database style plugins for winamp, i think.

maybe foobar can do it, but i'm embarassed to say i've never tried that.