This is a really tough call between Begins and Royale. I'm going to give it to Bond because while Begins was a terrific film, there's one scene in there that delved into Episode I territory (and I think alot of you know what I'm talking about.) Everything else about it is almost dead perfect and it does hold up well but that one scene sort of hurts. I also agree the plot with the fear gas was a little unnecessary. Those things don't damage my viewing or opinion of Begins, but I do notice them.
Casino Royale was probably the best action film of 2006 (if you don't count Miami Vice or The Departed.) I was VERY skeptical and in some ways wrote off Craig as the new Bond but not only did he prove me completely wrong, I'm now counting down the days until the next Bond. That's something I never did as I never cared for a Bond since GoldenEye. Yes it was like the Bourne films, and yes Bourne Supremacy is still better but Casino Royale gave a big shot in the arm (much like Begins did) to a franchise that needed it. All the acting in Royale was top notch and Martin Campbell isn't the greatest director, but he did get the job done and got it done very well.
Superman Returns is a completely different matter. I love Superman, always have and think the first film has the one of the best openings and closings you're ever going to find in a film. Returns managed to mess both of those things right up, but that's not my problem with it. My problem with Superman Returns stems from the one scene where it falls apart in a split second. I'm talking about something that involves a boat, a child, and a piano. It's about there where I realized SR doesn't know if it wants to be an action film or a drama and the film suffered greatly. I liked Routh, I liked Spacey, and certainly Bosworth looked gorgeous, but the overall film lost itself an hour and a half (roughly) into it. Everyone talks that Casino Royale ran on too long, well so did Superman Returns. Explain how Superman can lift and entire rock of Kryptonite...the thing that weakens him. Explain to me why we're taking Superman in doors when it's been documented in even The Dark Knight Returns where he gets his power from. Explain to me why the radiation of Kryptonite that big isn't making Clark weaker and drowsy. Superman Returns didn't know what it wanted to be, be it an action film or a drama and the film suffered big time for it.