Apple default apps. At least when I had my iPod Touch 2G, some apps simply needed a device restart or they would not perform well at all. Simcity for example, was the one I always noticed.
To be fair, there's actually a large number of reports of crashes and freezes in the App Store. I wouldn't consider SimCity Deluxe for iOS to be a model citizen in terms of application stability.
If I trawl through all my logs in Xcode, the number of app crashes I've seen with the iPhone 3GS, iPhone 4 and iPhone 4S from third-party apps can be counted using just the fingers on my hands. I think there was once an application that proved to be a bit unstable, and it ended up replaced by an alternative pretty quickly.
You're right. I didn't jailbreak, but I remember having the same kind of issues. I found that Worms would run much better if I restarted the phone first, I assume because it was easier to allocate contiguous blocks of memory.
But it's a game by game thing. I don't remember ever having problems with Flight Control or Peggle. Even some fancier games don't seem effected, while Angry Birds would hit the problem. Interestingly, Angry Birds would get better if you went to the level select and then back into the level.
Which is why Apple did not enable it on the 3G in the first place. (did you jailbreak it, or are you talking about the 3GS?)