Personally I like .MKV(Anime files - Multiple channel sound and subtitle options)
But, I have to say, even if you never heard of it, .OGM is pretty good. It uses OGG audio and the video is smooth etc. It has subtitle support and such but I use .MKV for quality purposes. .OGM goes on my Personal Media Player
I don't really use small size formats like WMA for music etc. I like quality.
What do you need this for? If your putting video's on a iPod you can only use one format.