Rich and Bob are cut from the same cloth. You should be able to go into the various apps that have files and delete them no? My understanding is that if you delete an app the files go with it. No empirical proof of that though. One of the nice features of iOS 5 is that it actually shows you how much storage space the data from each app is using.
I'm in the middle of the Recovery right now and I'm going to set it up as a new iPad (I can always restore it from backup later). I want to see how it runs on a fresh install of iOS 5. I'll post back...sooner or later.
And you should be able to do it un-jailbroken. It might be an interesting test to see what is kept and what is deleted when you delete an application. More to the point, over time, is enough stuff kept that can/could affect the performance of the device? Sixteen Gigs is huge, but it is also finite
In Winders, lots of stuff remains when you delete an application. I installed and deleted a graphics program that left several folders and a bunch of graphics. Many programs leave bits and pieces on the HDD. I have 400 plus gigs of space on my laptop, so it is not an issue. Then again, delete means delete. Or it should.