carvin do
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warmoth.com do, but you have to assemble them yourself
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Do you mean by all the parts online or make a mock up of a custom guitar?

If you just want a mock up google kisakae

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It depends on what you mean. If you mean mock ups then kisakae is pretty good, I tried that.

If you mean wanting to get a custom built guitar it depends because there is a difference between custom and semi-custom.

With custom, pretty much any of the major guitar manufacturers have a custom shop. However, you will pay a lot and you may be able to get a well built guitar for cheaper from a local luthier.

If you want semi-custom there is Carvin and Warmoth and a few others. Not quite the same thing as true custom, in that you are limited to using their standard parts, but it is much cheaper than true custom. The easiest way to tell the difference is if they have any type of price up, true custom guitars have to be quoted case by case, so they won't put a price up.