I'll let someone else try to tackle specific recommendations. I really don't know much about gear at that price point.
Another problem is that the right speakers for you depend a lot on your listening environment, your listening habits and what else you might care to do with your life besides spend money on A/V gear.
Here are a few suggestions to help you find the right stuff:
1. Start by figuring out what kind of speakers you want. Free-standing towers give you the best range of sound, but can be big & bulky and might be overkill for a small room. Bookshelf speakers are a good compromise for smaller budgets or smaller spaces. In-wall or in-ceiling speakers can give you the cleanest look, but may require some compromises in sound quality. Finally, HTIB systems are good for very tight budgets or people who don't care much about sound quality.
Based on your original post and the other gear you're looking at, I think a HTIB is the wrong way to go.
2. Go listen to some speakers. Bring a few CDs of music you really like and listen to stereo setups. Stereo music is a great way to audition because it's plentiful and detailed and will give you a good feel for how different speakers sound. When you find 2 you like, the other 3 should sound the same.
3. Your subwoofer doesn't have to match the other speakers, but the main speakers should all be the same brand and of the same family.
4. This is my opinion, but since you mentioned an interest in quality, go listen to some more expensive speakers. At $1000-1200 for a 5.1 system, you're talking $200 or less for each speaker, so listen to some speakers in the $3-400/ea range. If you hear a difference in sound quality worth paying for you can always get more expensive L/R/C speakers now and pick up the surrounds later, or re-evaluate your budget and save for something nicer. Its better to know what you're getting and be happy with it than to focus too much on cost and regret what you didn't get.