While I rarely ever play online, and have never participated in an online league, I have in the past contemplated some different format ideas.
An idea I have once considered, similar to stalltalk's, is a draft that would unfortunately necessitate a two season commitment from league members: you seed the league members, in this example, from one to 28. Then members each choose one roster for their second season, but their choice is countered by an assigned team for the first season. The assigned team is the team selected by another league member by reversing the draft order (first selection pairs with the 28th, two with 27, three with 26, etc., etc.)...
In our example, we will say that 'stalltalk' chooses the Giants will the first pick; 'Jebigred' takes the 49ers second; and 'vikingmoe' selects the Vikings third. Then, at the tail end of this draft, we'll say 'suicideking81' lands the Packers at 26; with the 27th pick we will say that I grab the Patriots; and with the final choice 'hoffnasty9' winds up with the Colts.
Meaning in season one of two, 'hoffnasty9' gets the Giants, and then in year two does his purgatory with the Colts:
S.F - Lurch
GIA - hoffnasty9
Plenty of different ways to interpret and to even alter such ideas, but I thought I'd pass the general premise along. Have fun, folks.