A Daily Planet website would be great, similar to the Gotham Times and the HAHAtimes that proved to be a red herring/April Fools by the Joker.
Via the Daily Planet, especially Lois' articles, we could keep up with the latest news on Superman and Metropolis. Just think about it... Articles about a new possible threat, whispers about Luthor's whereabouts, the public's opinion on Superman's return, etc. Lots of possibilities here.
I've seen someone suggest a game like "Where is Superman now?" (similar to "Where in the World is Carmen Santiego?") where fans would have to track him down based on the given clues, either from press reports, Lois' articles, "word on the street" (other viral websites), etc. Maybe there would be clues hidden at different places in the world ("Superman was here") and collecting them all would help us reveal his current location.
There could also be a Clark Kent game involving scoops and fetching things and "beating others to the game". "Be the one to get the main headline!" and the like. There's SO MUCH stuff you could do here. It could be just as interactive as The Dark Knight ARG.
How about solving puzzles to reveal the latest Daily Planet headline (with a secret message that leads to a prize/a new picture/etc?)?
It's not that hard at all to come up with ideas, really. It's all about giving fans the chance to connect and play the games as one big group. It's more about community than marketing the film. The fact it helps the hype going (and HOW!) is just a bonus.
EDIT: Also, I'd love to see a viral website of the Daily Planet's rival newspaper(s)! People could submit news to whichever newspaper they like best.