How does your saving system works like? I'm not entirely sure, but I think that large amounts of individual saves can have -some- effect. It might be worth the time tidying them up a bit. If it doesn't improve performance, you've got a neat und tidy saves list, at least.
Was Skyrim fine from the beginning and got chugging once you began modding it? If it was, it's a good idea to slot them in and out, trying to find the culprit and take it from there. If you don't know, slot out all the mods and see what happens. If it's the vanilla game being uncooperative, try lowering the settings and keep an eye out for dedicated performance mods.
The Unofficial Skyrim Patch is great, but the performance gain isn't the main benefit of that mod.