If it has actual IMAX footage in it (Chris Nolan, I'm looking at you), then IMAX any day of the week.
I think the problem with 3D is the lack of good 3D in movies. Sure, there's Avatar and Titanic, and a couple of other movies also look pretty good, but for the most part it's just silly 'stuff flying out of the screen' Resident Evil material that doesn't matter if it's seen in either the second or third dimension.
Having said that, if I'm going to watch a movie in 3D, I'd prefer to see it in on an IMAX screen. The added size helps sell the 3D effect. If you sit in the right place, your peripheral vision is obscured by the screen, so it really feels like you're looking at something with depth.