i have a 3000gt and im wanting to change up the stock audio system that it has.. i wanna do something custom so can anyone help with ideas.. thanks...  

personal preference but i would say alpine deck, hertz speakers, jl subs and jl amp. i had the same set up in my old car but with premier subs  

I'm a big fan of Alpine too...but i'm putting in a new Diamond Audio system for my car.  Their not the cheapest but I have never heard anyone complain about the quality and sound.  Very, very good amps and subs!!  

personally i will never run an amp besides jl. they're indestructable and put out tons of power. as far as subs though they change so much from year to year so you kinda gotta check em out eh  

As far as your sub box goes I would look on ebay they have nice custom boxes that fit your rear hatch perfect, you can even choose the color of the carpet to match the rest of the car. Not many boxes will fit the 3000gt being they have such little trunk space. As for brand you cant go wrong with JL or kicker, and dont forget the dynamat.  

Look into fiberglass housings for the trunk build. It's a fairly light material and can be molded to fit inside the trunk area with speakers. There are plenty of brands out there that put out a lot of wattage for sound. I like ZUES products, my self. But that's my preference.
I ran a 1000w, 4 chanel amp with 4 12" subs and another 1000w, 6 chanel amp to power the rest of the systems needs, i.e.; lows, mids and highs. In total I remember having 10 to 12 speakers in the car. Including the subs. The head unit was a 50w per chanel Pioneer. All power was fed through 2 and 4 gauge wire harnesses with relays, circuit brakers and 4 10farad capacitors, 4 equalizers and a sub splitter. The alternator was rewound and refabricated to put out 150 amps, regulated. They cost me a lot of money. The caps were custome made by a company that is now defunct due to the economy.
I lost the system in an accident that I wasn't a part of. This is why you never lend out your car to any one. Literally, it was a crash and burn. My friend survived but not my car. It was a 97 Honda wagon. The cause of the accident was a drunk 18 year old that got his licence on his birthday. Way to show responsibility! Good thing the insurance payed for my loss. It pays to document with receipts and to physically have the car inspected by your insurance company for value. Full coverage, baby! It pays!