Perhaps your list is more informative as to what you DON'T have listed!

I have TWO (2) N800's.

One has all of my applications on it the other is essentially BARE (OS only).

The difference in speed between them is significant and agrees with your observations.

Too much installing/uninstalling applications which may or may not be "well-behaved" (in terms of cleaning up after themselves!) can have a negative affect on performance.

There are one or two applications that I have on my "fully-loaded" N800 which I suspect are the main culprits in some of my problems: speed during browsing and making a reliable WiFi connection. I won't mention them here as I haven't been able to draw a conclusion yet.