Best 1,000 complete system for girlfriend ideas

The basic criterion for WAF (wife approval factor) or in this case GAF are
1 Is it pretty?
2 Can I make it function with the push of 1 button?
3 Is it small and does it fit in with the decor?
There are those who have posted above who have mentioned these various aspects of the typical woman's psyche. You would be wise to heed their advice. You may get her the best possible sound for $1k, but if she can't get it to function easily you will definitely hear about it.
Contrary to Sean's 2nd post, Do Not let her see Bose. She will think she can hide them and thus take care of the "pretty" problem. Or she may think they are cute (remember small is good). SD has mentioned the Teac components. Most likely the gold anodized finish will fit into the decor better and will be more appreciated than black boxes which don't match the carpet or drapes or sofa, etc. If you can get these features and good sound you have done well grasshopper. Remember great sound is what you want. Give her what she wants with great sound and you may make an audiophile convert. (although I don't know if you've done her any favors seeing as how she was satisfied with Best Buy's best and now it will take $10-25K to satisfy her addiction)
These observations are based on 26 yrs of marriage in which I am always amazed at how 2 people can seem to think so differently and so much alike at the same time.
This may not help determine the exact system but it may help to keep a girlfriend happy, and her happiness will help determine your happiness. YMMV

NAD receiver (7100?), B&W 302 speakers, and splurge on a used Cal Labs ICon cd player, don't forget just above budget interconnects and speaker wires

have fun

I agree with the above...skip the seperates and buy an integrated, or a receiver (with remote). They're probably right. She may learn to appreciate the improved sound one day, but it will need to be convenient and sensibly set up for her to use it regularly. There are plenty of decent receivers out there...like NAD, HK, Onkyo, Yamaha, Rotel, Marantz, etc. They may not be "high-end", but they're all relatively well made and they won't cause your ears to bleed. The speakers are probably the most important as far as the sound goes, so you may want to present her with a few options and let her choose the ones that she prefers (based on sound and looks).

Buy an Integrated amp,you get more bang for you buck than seperates.
For 329.00 you can buy a brand new NAD T550 DVD-CD player from Upsacle Audio.
Your well on your way.

If you're worried about "matching the decor," remember that the Linn Classik is available in about 7 colors; also the B&W LM-1 Leisure Monitors are small, have their own little integral stands, and also come in various colors, including white so you can mount them on the wall (probably not acceptable).