I've been really happy with my Pioneer AVH-X3600BHS. It has subwoofer controls and the connections for it, built in HD radio/Blue-tooth/DVD and reverse camera input. there are better/higher quality units out there that you can spend a bunch on, but you can find these for $260 now and I've had mine for 2 years now without any issues and am really happy with these paired with some infinity speakers.
Any of the "brand name" head units would likely serve your needs. Personally I would stay away from the entry level stuff like Boss, Pile, Sony, Dual, etc.
If you are thinking about adding amps later, look for something with at least 4 volt pre-outs, it will drive the amp much better with lower noise and less distortion because you will be able to leave the amp gain control turned down much further. Just the 4v pre -outs alone will weed out a lot of the brands I mentioned above. 3 sets of pre-outs so you have a dedicated channel with level control for the sub is nice too, like ZRXKuma mentioned.
When you get to amps and speakers, I would suggest 6.5" round using adapters for the oval holes in the doors (you can see how they install in my work log below). You will get better sound off of round and much more selection in decent speakers than with the ovals.
For amps, yes, I agree with Dieselfreak77, hard to beat JL but be prepared to pay a premium for them.
For speakers, you really need to audition them if at all possible, a spec sheet will not tell you how they sound and if they will suit your taste. I installed a set of 4 Infinities originally in my truck back when it was new. I found them too "bright" for my taste, I am now running 4 JL Audio 6.5" in the front doors and I love them...but I had to replace the JL tweeters with Alpines because they were also to much for my ears. I do love most of the better Alpine speakers as well like the Type "R" and higher series, they have one of the most natural sounds to me.... but again it's like saying what is the best color of truck, it's all a matter of personal taste when it comes to speakers.
Good luck with your search, ask more questions if you have them, otherwise I hope you post some pics of your install when you are done!