I like the recommendation of the Denon 2313. My 2309 model has served me very well. Yamaha and Pioneer and Onkyo each have their pluses and minuses. Onkyo has great specs and sells street price for big discounts over MSRP. Lately their rep has taken a hit due to poor quality, overheating, and bad customer service though. Yamaha and Pioneer both use their own room correction software, while Denon uses Audyssey, which most people on this forum seem to prefer.
The Deftech Studio monitor seem to be getting a lot of positive press and you should be able to demo those at a BestBuy near you.
I would avoid the Supercube sub though, it is way overpriced. For an apartment, check out the new SVS SB-1000 for $499.
Hsu makes great subs, but I did not love their speakers when I heard them. Also, that sub would probably be overkill for your situation.
For other speakers, check out Aperion Versus line or Ascend Sierras.