I don't have GPS on mine and have never flown a craft that did. I could see it being useful as a failsafe and for GPS lock if I was doing aerial photography. But don't let it get in the way of learning how to fly your craft manually. I've heard too many stories of people who only knew how to use the GPS and when it lost satellite lock they freaked out and ended up crashing it.
There are as many different builds are there are quads that have been scratch built! Search YouTube, this forum, FliteTest.com, RCGroups.com, etc. See what other people have done and get some ideas of what you like, don't like, etc. Come up with a plan and then carry it out.
Decide what size you want and how much work you want to do and go from there. Do you want to buy parts and just assemble? Do you want to hand make as much as you can? I scratch built my own wooden frame for my 500. But I bought an FPV250 frame from HobbyKing for my son. I really like both.
Research flight controllers. The KK Board is very well documented and I have friends that love theirs. MultiWii based boards are really leaping ahead in my opinion, though. I really like the Naze32 flight controller (actually a Swift32 clone of it I got from ReadyToFlyQuads.com - awesome guy to do business with). GPS support is still a little undercooked on that however, from what I understand. It's getting better, though. If GPS is important, then you might want to look at APM or DJI's Naza, but that's more expensive.
Motors, ESCs, props, etc. really depend on what size you want to build. The bigger the props, the slower the motor (lower kv). Get ESCs that have a slightly higher amp rating than the motors. My motors are 1000kv, props are 8" (but I can go up to 10" if I wanted), my ESCs are 20A. My son uses 5" 3-blade (I've been trying to talk him in to getting 6" 2-blade, but he really likes the 3-blade), 2300kv motors, and 12A ESCs. We both use 3S LiPo batteries - 2200mAh for me and 1300mAh for him.
I went cheap on my radio. I have the Turnigy 9X from HobbyKing and I don't regret it. My buddy spent a lot on a Hitec Aurora 9. And although he does like it and it's a great Tx, he wishes he had bought the Turnigy and spent that money on other things.
Come up with a plan. Create a build list. Post it here and get feedback. Have fun!