Ok, I have driven Emory NUTS with questions on this kind of stuff, so I'll post what I've learned here. I'm going to leave out any prices because they may be different for different hilts and I don't want to speak out of turn.
Colors: Custom colors that have been commonly done are Sentinel Yellow, a bluer Violet Amethyst, and Pyrestone (a red-orange color). I think you could go gold also since that is what the RGB yellow turns out to be.
Claws: As far as I know, Ultra doesn't do any custom claw work. You can order Raven or War Glaive claws to use for your own mods though and they are a great starting point - that's what I did with my Prophecies and I'm looking to do a friend's liberator with 3 WG claws as well.
Hilt: You can have rechargable batteries w/ recharge port custom ordered. It's a little over half the cost of going RGB as far as I know, so not cheap but not bad. Ultra will also install LEDs to shine out of the pommel if you want. Both of these options likely require a different pommel.
I also have prophecies and being MHS compatible is definitely a plus for some of the mods. These are all I know of but I'm sure there are more. There are definitely custom sound mods, but I'd hold off on that until Ultra finishes whatever he's working on for the new sound option (he's given that advice to a few others here on the forum).
Navajas' Custom Prophecy LE - Yellow / Recharge / EconoSound / Greeble http://www.saberforum.com/index.php?topic=1096.0My Custom Dark Prophecies - Pyrestone / Clawshttp://www.saberforum.com/index.php?topic=1306.0