Since you're already getting tons of ideas thrown at you, here's another.
I'd echo some of what Knownothing and Zigonht and others have mentioned. Also, this is based on my own experience as someone who went down this path of wanting a good HT system and a very good 2-channel audio system. Use a receiver to power the center and rear channels. Use the pre-outs to a good used 2-channel amp to drive the main speakers.
Get a decent HT receiver (5.1 would be good) with a set of pre-outs. I'm using an Outlaw 1050. (Used receiver for less than $300.)
Very good set of full range used speakers. You can find a set of fantastic speakers on this site for $1500 or less. I use a set of Thiel 1.5's.
Used 2-channel amp. Some of the older ones are built like tanks, are inexpensive, and sound great. You can get a really nice older SS amp for under $500.
For the center and rear speakers, I'd get a decent center and some so-so rears. I don't get too terribly concerned on matching the rear effect speakers up to the other (except for volume balancing). With certain receivers, you can phantom the center channel by having the sound emminate from the two mains, but, I think having the center sounds better for HT. You can probably get a set of rears and a center for under $300.
So far were around $2600. With the rest of the budget you could get a powered sub (if needed), a source component, and some decent cables. On cable, I've found that moving up from the crap that ships with components is absolutely necessary, but, one does not need to move into the $100+ level for interconnects and speaker cables for good sound.
Have fun.
Chris