Here is a scenario and the flawed implementation:
People asked to open all apps into the same state after a re-boot as before. Yes, that maybe useful in some cases. So Lion implemented it.
I don't like it as my main tools will be often different each time. What am I complaining here. There is this great checkbox to disable it, right?
1. This checkbox is not sticky
2. If another computer is connected to your machine (and my Air is most of the time) this option will never show
3. If you have a UI freeze (I had one today) all the apps that were open before will open again and this maybe even the cause for the problem in the first place.
Keep it simple and never try to be too clever. Lion wants to be way to clever here. If I could disable it no problem. Doesn't seem to be possible.