If it's complicated at all it's just because there's so much good stuff out there to choose from!
Given the ubiquity of receivers and the relative rarity of integrated amps, I'd say a receiver is the way to go. There're many good models that would meet your needs for under $200 new (you do live in the US, correct?). Used could be a great option, too. If you shop Audiogon, or eBay, being careful to stick to those with good feedback, you can get really nice clean used stuff for $.20- $.50 on the dollar. All the big manufacturers release new models yearly, or even more often. So the previous model used is usually a great deal, especially since you don't need or desire all the newfangled bells & whistles.
If used makes sense with amps, it's doubly true with speaker. There's more to go wrong with electronics, but speakers are generally very very safe buys used. Provided they haven't been abused, and are modern models with rubber surrounds or new foam, you should get many years out of them.
It's hard to recommend specific models. The Athena line is a great value, even new. You could probably get 4 towers and a decent receiver for about the $1000 you cite as your budget. Alternately, you could buy a bit nicer reciever and speakers now, along with a nice entry CD player and add a 2nd pair of speakers down the road. You'll be much happier with one good pair than two mediocre pairs.
Do a bit of reading here at AH, then check out Audiogon. Look for prices of the stuff that interests you. One note, though- Agon tends to deal mostly in higher end stuff. You may not find much for mass market stuff there. Ebay is a better place to find those brands. But be very careful on ebay! Stick to sellers with a lot of good feedback.
Yes, there's good deals on new gear, but don't overlook the used market. Just like with cars, there's a lot to be said for letting the first own take the big hit from depreciation!
