I'm going to chime in here...
First, for plenty of ideas check out the $1000 Audio Challenge sticky thread. However, many of the posts in that thread asume people want subs...which I agree, is not always necessary. A set of 6.5" components properly amplified can yeild great results at moderate listening levels as long as you don't enjoy Rap/HipHop. Additionally, you mentioned 1000+ as your limit so since you're looking for SQ (which doesn't come cheap) I'm going to make use of the '+'. I'm also going to asume you don't want to scour ebay for months waiting for the best deal...so this is a new equipment suggestion.
So here's my recommendation...
You mentioned you don't want anything flashy for a head unit. For around $275-350 you can pick up a Nakamichi CD-400. Its a no frills head unit that is all about SQ.
For amplification, I would find a 2 channel amp that puts out about 75-110 watts per channel. Since you don't have to overcome your desire for loud bass like most car audio enthusiasts the power rating is less important than the quality of the amp. I recommend the Zapco Reference 350.2 (100x2) for $469.
Finally, for your components, you're going to want something that will sound great running full range. A set of 6.5" components is a must. If you're up for some fiberglassing you could move up to a set of 3-ways but that may bust the budget too much. So for the easiest install I would recommend a set of CD Tech Eurosport 6.5" braxials. You can pickup last year's model for $500 at
www.mmxpress.com. They are regularly around $650.
Of course you need wiring which you can pick up at
www.knukoncepts.com for around $100, maybe less. Then there is the install materials. I'll guess around another $100 for miscelaneous stuff: carpet, mdf, screws, glue, jig saw blades, and all that other s*** that adds up.
My grand total:
Nak CD-400 $350
Zapco 350.2 $469
CDT ES 6.5s $650
Wiring $100
Misc. $100
Total = $1669
That my friend would be a sweet system. Anyone that listens to it would not be asking "where's the bass" ... unless you put in Jay-Z's latest album that is.