1. It could be the End of the World arc, but someone else noted that a movie with pretty much just two characters might not go over so well, regardless of how popular one of those characters is. Also, this would probably mean they're dumping everything between the end of the second season and the start of EotW, which is sad.
2. Greece Arc - fillers could also work, but I liked the fillers, so I'm hoping they save that one for a full season. That's what I didn't really like about the second season; they dropped a lot of my favourite chapters (my Risa chapter ;-
3. Saw someone else saying it'd be a remake of the start of the series, which isn't very likely, unless they're doing something like making a version to match the second season's continuity.
4. It also might be a non-canon thing made to bridge the gap between two seasons, like that OVA they did. Don't really see why'd they'd use an entire movie just for that. Also, of course, there's been no news of a third season. (I suppose they could be using the movie to get suport for one, though....)
5. I think HnG is now officially playing
animation studio roulette. Here's hoping they hit Studio SHAFT next! (Or Satelight. I have a soft spot for Satelight....)