I had put a full set of Alpine Type-R components all around in my friend's 4th gen. F450 4ch alpine amp, and then one single 15" Type-R sub in a custom built ported box with an alpine PDX series 1000watt rms amp with 3 1 farad capacitors. And for the deck we went with a 9853 Alpine. He had to buy everything retail cost which ran about 2800 or so. It was quite nice, but that's a bit extreme. The problem with getting Type-R components is that they just barely fit in the doors depth wise and width (6.5" models).
If you don't want to go crazy I'd recommend (if you need a deck) an Alpine 9846 which will run you around $150. It has preouts just for subs, so if you ever decide to get a 4 channel amp setup, you will need a new deck - but for the average person, it's unnecessary. And for speakers, Either go with Alpine Type-S's which will give you a decent frequency range, kind of a middle of the road speaker, you get bass and highs. They are around 100 a pair. If you are definitely getting subs, I would recommend getting some Pioneer 3 or 4 way speakers. They don't handle bass well - but obviously you won't need them to. They are a bit cheaper, around 80 a pair. If you wanted to, you could get the speaker grilles for the rear deck out of an older accord (I actually have a pair laying around) that can take 6x9's, just check the clearance of the hole in the rear deck.
As for subs, if you want a decent mid level system, I'd probably go with rockford for the subs, some nice Punch P2's with dual 4ohm coils. And grab a rockford Punch 450.2 amp to go with it. That's what i had put into my girlfriend's car and it pumps - you will definitely need at least a 1 farad capacitor with that amp or you're going to be damaging the subs at high volumes. Those subs and amp will run you probably close to around 600ish.
If you want to step down from those, I'd jump to Alpine Type-E's or Type-S's. Either of which would fair well with the M450(400rms @ 2ohm) mono block alpine amp. However you could juice them up a bit more with a bigger amp as well, such as the M650(600rms @ 2ohm).
Currently I run two 12" Type-R's and two MRP-M650 amps for the subs in my accord in a vented box. It kicks very hard, i'm glad my mirror is attached to the roof and not the glass