One nice touch is that the end scene is almost exactly how Doyle originally ended things.
Holmes was apparently killed by Moriarity, going over a cliff while grappling with him. The original intent had been to actually kill off the character, as Doyle was tired of him or something, but later brought him back.
Moriarty was a great character. Cast just right, which is nice since I don't think I'd seen that actor before. I felt like there was a bit of a copout with the reveal near the end that Holmes had
figured things out and basically wrecked Moriarity by figuring out his accounts.
It could've used a few comments or bits here and there to give more background to Holmes figuring it out. It wasn't entirely out of the blue, but I think a couple more bread crumbs for the viewers would've been nice. On the other hand, the adrenaline was an obvious Chekov's Gun. Maybe it balances out.
And what was with the scene talking about the Holmes brothers' secret code in messages? Did that come up anywhere else? I'm hoping it's a setup for the next film, which is supposed to be out in December 2013. Otherwise, beyond the "naked fat man haha" angle of that scene it seems a bit pointless. They could've cut it without losing anything if Mycroft had told Watson in Switzerland, "Oh, your wife is doing great also she saw my flaccid penis and I have a really old butler."
In fact I may have preferred that, if only for the magic and whimsy of that line appearing on Youtube forevermore.