As of the Innistrad Release online, Commander has had a couple changes online (announced 12 Oct 11).
Multiplayer Games can now support up to 6 players.
1:1 Commander games can now be played in the Casual and Anything Goes rooms by selecting Commander in both drop down boxes (just like in the Multiplayer room). Solitaire deck testing is only available by making a 1:1 game and closing entry before another player joins.
Details can be found here: