Ok, it has been almost a year since I've posted this question. Lots of things changed, but the battery issue persisted through all the minor updates to 3.1.
The interesting thing is that ever since I've installed iOS 4 I see a radical improvement (25-30% more battery life) despite iOS4 being theoretically far more demanding on power and CPU. My setup did not change – mobileme push, 1 exchange and 1 imap email account. But now I can actually finish a whole workday without having to kick the juice-pack in or plug the phone into the wall.
Let me be very clear: we're still talking about battery life that is nowhere near Apple's specifications, but it is at least useable enough. The only thing I did during upgrade was to delete all my email accounts and reboot before upgrading, followed by a clean re-setup of all the email stuff. I suppose that does help as iOS4's Mail.app is quite different from its predecessor and setting it up from scratch might come useful.
I also have the problem but I just removed it. I closed all webpages I have visited in safari and made safari clean and turned iPhone off and checked after a day. Astonishingly, my iPhone regained its old performance. Great. *Note: I usually visit my gami account in safari. I think this may be the problem.