Two words: Impedance Matching.
At this point, buying preamps and discrete (seperate) audio components may well be getting you in too deep. There's a lot of knowledge you need to have before you try to do anything in that route. Especially since you're talking about 4-ohm speakers. Almost all consumer-level equipment is 8-ohm
If you use different impedance equipment (say 4ohm speakers with a receiver rated for 8ohms) without taking into consideration all the factors, you can easily damage or destroy your speakers and the amplifier section of your receiver (or discrete amplifier, etc etc) It is possible to run mismatched equipment but speakers have to be hooked up in groups (bye bye 5.1, hello 2.0 on 6 speakers) and they need to be hooked up very specifically. There is such a thing as a bridgeable amplifier, but no, you can't hook two high-ohm receivers together to run a low-ohm speaker. As for how much power you need, 100-150 watts per channel is more than enough for most people's home theatre. Go much above that and you'll be getting the cops called on you for noise complaints.
You were asking me about running this system for listening to mp3s and downloaded movies off your computer. To be brutally honest, you're going way overkill. The Yamaha RX series receivers you were looking at were perfect for what you're wanting to do. Even they might be a bit overkill. Buying $10,000 worth of equipment is overkill, period. Let me tell you a secret: 50% of the price on this stuff (speakers especially) is brand name alone. Starting off with a quality receiver, and a nice set of floorstanding or bookshelf speakers is all you'll need. If you start messing with preamps and discrete components, you're going to be opening a can of worms.
My advice is to buy an 8-ohm receiver and an 8-ohm speaker set. Why? It's the most common impedance. You'll have a much easier time selling an 8-ohm set to most people if you ever do upgrade, or if you buy a new set and move the old set to another room, or replace a speaker or two it will be much easier to find compatible products.
Don't get me wrong, there's nothing wrong with using preamps, discrete tuners, decks, and amplifiers if you know what you're doing, but that takes quite a bit of forethought and knowledge and gets REAL expensive, REAL quick.
To sum it up:
Don't go with the Klipsch HT1000 speakers, if you're worried about sound fidelity. Chances are you'll be missing some of the mids, and the only lows will be coming from the sub - like your logitech system.
Don't buy the most expensive thing you can find, just because the reviews are great. It takes a trained ear to tell the difference between mid-range and high-end stuff, and it's near impossible to tell the difference between high-to-ultra high end stuff in terms of quality. Different brands and models will have a different sound
color which might be easily distinguishable, one might sound "bright" another "warm", but most if not all should have a "good" reproduction of the sound spectrum. Unless you already have a very specific picture of what you want your speakers to sound like (and you've pretty much proved that you don't) then the price difference isn't worth it. This right here, the hopping around between reviews is why I recommended you go to a store to listen. You can't listen to the speaker online.
Look to be spending between $100-$200 per speaker. I really recommend 8-ohm speakers and equipment, or if not, at least buy impedance-matched equipment (4-ohm speaker to 4-ohm amp)
When it comes to Preamps, preouts, etc... I don't think you need it. The amplifier section on any quality receiver should be more than enough, both in terms of power and quality. You aren't planning on running an actual cinema, are you? If you really really want the option to add discrete amps later, go for a receiver with pre-outs (such as the V667) like robert-the-rambler suggested. My vote, however, is to go with the RX-V471 you had picked out, (or the V571 if you want 7.1) I don't think you'll be disappointed.
It's important to note, you need a seperate amp (or at least seperate amp channel) for each channel of the 5.1 to use the preouts (not including the subwoofer, as that usually has a built-in amp). That's 5 mono amps or 3 stereo amps or a very expensive purpose-built 5-channel amp for 5.1 if you use discrete amplification.
Download some FLAC or other lossless audio to try out. Your music may very well just not sound good because it isn't good.
Logitech speakers are not very good.
PC audio isn't engineered for high fidelity. Logitech doesn't use tweeters and their speakers have no resolution, detail and the bass is over powering and loose.
http://forum.blu-ray.com/home-theater-construction/57127-speaker-cable-sleeving-diy.html
Careful. A more accurate statement is: Devices marketed as "Computer Speakers" aren't engineered for high fidelity.
PC audio can very well be high fidelity, if done right. My father's Digidesign and Presonus PC-based studio audio recording equipment dispute your statement