The following is a compilation of some of the sites that carry custom 1/6 scale items I frequent most. For different reasons described below, these sites are a valuable resource for the 1/6 community. A lot of the links you see below are from regular Joes like you or me.  They provide invaluable services to other collectors for "the love of the hobby" and they often do it as a side hobby and not as a main source of income so if you ever decide to buy from any of them, please keep that in mind.

Lonnie Hale's Hero Heads
I have a lot of respect for Lonnie Hale and Jim Maddox. Many people think he makes a killing recasting all those heads and selling them, but until you actually commission a job by Jim Maddox or another sculptor, you won't know how hard it really is. I give him a lot of props for doing this as a hobby and providing us 1/6 scale hobbyists with something that's a total work of art. The sculpts you see on Lonnie's Hero Heads are made by Jim Maddox, a professional sculptor (who also occasionally browse the boards as "Edylhands"). Jim's talent is almost unparalleled and he has done a good deal of headsculpts for professional toy companies such as Dragon and BBI. Another comment I'd want to add is Lonnie's casting - it is definitely the best cast job I've ever received. I buy stuff from eBay, trades and everywhere else and no one has come to match the quality of casts as Lonnie's. They are bubble free (this is extremely important especially when you are painting) and are very durable. I've bought casts before from other sites and have received big air bubbles in the eyes and nose. If you can imagine a huge hole in the middle of your figure's nose, it ain't a pretty sight.

Jim's Printable Minis
This is a great site for making your own dioramas and printed 1/6 scale materials. You can make tons of cool stuff like pizza boxes, cigarette boxes, movie posters, police badges and even money with your own printer. It's certainly a lot cheaper than buying it that's for sure.

Adventure Gear
For the customizer, by the customizer. Started by Tom Calhoun, the site offers a lot of 1/6 clothing that is custom made. Although their primary clothing line is for the Joes, they still fit a lot of Dragon and BBI figures as well.

Project ARE
Skip and Robin Are started this site. If you don't feel like sewing your own clothing, check out this site. They custom make clothing to fit Dragon, BBI, or G.I. Joe at your request. The fit is perfect and the prices are very, very reasonable. I've bought tons of items from them before and service is top notch.

Civies
Kris' site offers 1/6 scale suits. These are definitely some of the best suits I've seen for 12" action figures. Nicely detailed and tailored like a real suit.

Poppo Toys
Another head sculptor/castor, Bill Kern has offered many 1/6 hobbyists the opportunity of seeing the "human sized breasts" on his site instead of the silicone-induced boobs that come with the CY-Girls and Perfect Bodies by BBI. He also sells custom head sculpts of several famous stars.

Sovereign Studios
If you've got a lot of money, check out this site. Shawn creates some very impressive custom jobs, including a 12 inch Batman, Indiana Jones and The Mummy figures. The price may seem steep, but his work and dedication speak for itself and is worth the money if you don't want to do it yourself. For me, no matter whether I buy a figure that is custom made, direct from the retailer, or not, I still make some sort of modification to the figures so I almost never buy any custom figures.

Sixth Space
Here is Starcollector's site.  He offers a few pretty good actor sculpts.

Joe David Productions
This is the only place I know of that sells custom feet for the CY and Perfect Body girls.

1/6 USMC Aliens
Here is Chris Chulamanis' Aliens site. If you look for any sort of material to bash your Alien custom figures, you'll find them all here. Chris' intricate detail to the weaponry, armor, clothing and gear is simply astonishing. Prices are very decent for custom made gear.

Diorama Dreams
This is the mother of all diorama sites. Their prices for custom dioramas are very expensive so I listed them more as a reference site for use in making your own diorama.