Scripts, persistent refs, map markers that have had their names removed, AI schedules for NPCs, navmesh data in some cases, clutter that's been blown from its original positions, you name it. Lots of stuff gets added to the save over time. A lot of it will clear out on its own when cells reset, but the default cell reset for Skyrim is now 30 days and not 3 days so it can sometimes take a very long time for things to self correct.
Persistent refs never get cleaned out though, otherwise they wouldn't be persistent.
