I like StewMac for certain neat little tools,
http://www.stewmac.com/shop/Tools/Sanding_Tools_and_Supplies/Fret_Dressing_Stick.html
http://www.stewmac.com/shop/Tools/Special_tools_for:_Nuts_and_saddles/String_Lifter.html
http://www.stewmac.com/shop/Fretting_supplies/Polishing_and_abrasives/Fingerboard_Guards.html
and branded stuff like Switchcraft parts. They will skimp on certain things, they sold the bootleg Bill Lawrence pickups for years and they sell Fully-Finished Guitar Bodies with "spectacular quilted maple tops!" for only $195! Try and buy that at Warmoth....
http://www.stewmac.com/shop/Bodies,_necks,_wood/Electric_guitar:_Bodies/Flametop-S_Rear-routed_Guitar_Bodies.html
I'm not a big believer in the idea that I need Jason Lollar or Greg Kinman to custom wind me my own personalized $350 pickups to play "Suzie-Q" better on, but pickups (and tuning pegs) are about the last place I'd try to skimp out.