In many cases, I have been told that many materials for making homemade fixtures such as wood for fluorescent fixtures are a violation of the NEC code in the USA. Is there a way to make a permanently installed homemade non-incandescent fixture without violating the NEC code as I often enjoy the idea of designing and building my own HID and fluorescent fixtures to give them a unique twist to my dream house.

You can apply for an Underwriter's Laboratories approval on a case by case basis. If you do, however, be prepared to fork out lots of money as it is not cheap to do so.

Look up SPE-1000, field evaluation, or special inspection. The way it's done here to certify bespoke or low volume electrical equipment is to arrange for such a inspection to be done on each item from a agency such as the CSA or ESA here in Ontario. Equipment approved under SPE-1000 is considered approved for use by the authority having jurisdiction (AHJ) but does not constitute an official certification by UL/CSA. An equivalent program probably exists for the US. 

Bear in mind there is a cost associated with this process and you'll have to design and build your luminaires to meet all applicable standards.

Fortunately, I don't think that problem exists here. Any permanent electrical installation carried out by someone who isn't a qualified electrician officially needs to be inspected and signed off by one before it's connected, but I've never had any issues with that. We had an electrical inspection by the council (local authority, who we rent from) last year, and they had no problems with the work I'd done.

I don't think a 'wood fixture' would ever be able to qualify for code.
I've personally permanently installed homemade fluorescent fixtures, but made of sheetmetal. Probably the 'average person' wouldn't even know they were home-built. (a prow would obviously be able to tell, but in theory they should be just as safe as a factory-built one...)

I can't really claim anything about other jurisdictions, but I can detail the regulations in force where I live.

On paper it's not permitted to connect electrical equipment that's not been CSA-approved to the electrical system. But I remember reading in the Canadian Electrical Code that homemade equipment entirely made with CSA-approved components doesn't require separate approval for the assembled product.

Considering electrical codes are very similar on either side of the border, chances are there's a similar exception in the NEC. This would allow you to build your own fixture and install it permanently. But I'd make sure it's indeed possible first if I were you. 

@Foxtronix : Does this apply to plug-in devices as well ?

If it's a portable device, i.e. connected by a plug and not permanently wired, then I should think that (taking safety considerations into account) you can pretty much do what you want, otherwise how would us collectors experiment with different lamps and ballasts..? It's not reasonable and probably not possible to acquire a fixture for every single lamp and ballast combination that exists.

I just build whatever i want to build and NEC can go bother someone else.

Use common sense. If you think something might potentially someday fail catastrophically. Make it so it doesnt.

I just build whatever i want to build and NEC can go bother someone else.

Use common sense. If you think something might potentially someday fail catastrophically. Make it so it doesnt.

Anything may fail catastrophically, the question is how likely is that to happen and who would get the blame for collateral damages.
If nothing happens, nobody cares. And obviously it is the ideal outcome.
But if something does happen, mainly when contribution of something else gets involved (someone splashes or throws something on it by accident and it catches big fire), you may get in trouble for proving you have fulfilled your duty to made the design sound.
Using certified components according to their manufacturers instruction (so observing the material limitations for the fixture body,...; to ensure the certificates remain valid) is a way to fulfill that duty.
Getting recognized agency certification for your design is another way (obviously usable only if you want to produce them in quantity as a commercial manufacturer).
But otherwise you could fall quite short handed defending yourself in the eventual liability case, regardless what would be the technical merit. You would be arguing against lawyers, not engineers...