There are quite a few different reasons the phone might just slow down randomly, the one that seems to cause the most hiccups in Android is its built in garbage collection (google Android garbage collection for more info), which is when the phone tries to reclaim unused memory. Unfortunately, there's not much we can do about it for now. Kill any background apps, make sure the CPU doesn't drop too low, and see if you notice any patterns to the stuttering. This might help a developer figure out where the trouble spot is.
Android is still a relatively new phone Operating System, and there are still a few kinks to work out. Don't get me wrong, I love my Android phone, but if I'm honest, I'll tell you that both WebOS and iOS have a cleaner, smoother end-user experience. Additionally, the number of hardware configurations Android runs on is much greater, meaning that Google can't polish Android for one (or a few) piece of hardware until it runs perfectly like Apple or Palm.
The bottom line is that while it's not perfect now, it will continue to get better as long as developers continue to work with it.