Best thing I've done so far was replace my stock platinum plugs with Autolite 103 copper plugs. Less than $15
Redlinegoods.com has leather shift boots that are over $50 with shipping, but well worth it. That was my first mod and I can't even imagine not having them in the car now they fit so well.
For about $25 you can get foam speaker baffles from crutchfield to install behind your stock speakers. It is the cheapest way to improve the sound from the stock sound system.