Whether you are building a new guitar from scratch, or just need a hard-to-find part, these websites offer an incredible array of Guitar Parts and accessories.
Acme Guitar Works
Their flagship product is their Pre-Wired Pick Guard Assemblies, but they have fantastic inventory of guitar pickups, electronics, and hard to find hardware.
Imagine any part that you would need to build a guitar and they have it. Their inventory of guitar neck and guitar bodies is very impressive. Where applicable, they offer great options.
Pretty decent guitar parts at very reasonable prices
Probably the biggest and most impressive catalog of not only guitar parts, but also for any stringed instrument. They also offer instructional videos on how to build a guitar, pretty cool stuff here.
USA Custom Guitars
A small, but very cool guitar parts company who offer most standard parts such as guitar neck and guitar bodies. Excellent customer service.