Best $3,000 speaker/amp combo?

If I were you, I would do as I did :-);
Thiel 3.5's
Theshold S 500 Series II
+ money left over for a quality pre, ss or tube.

The used NAD M3 and BOSE 901 series 6 mk2's are two of the best bang for the buck products that you are likely to find for the money or for a lot more money. And they are a perfect match too!

Odyssey Audio Cyclops integrated amp. 110 Watts $995 ($1300 with upgrade)
Magnepan MG 1.7 $2000

Rega Mira $1200
Rega RS5 $1600

Exposure 2010S2 $1300
Dynaudio Excite x16 $1600

Nad C 326BEE $500
Spendor 3/1p R2 $2700

Hmm, I don't think there's any substitute for auditoning.

I'll just say that for that space, you'll want full-range speakers - you'll be sad if you get some bookshelves that don't go below 50hz!

If you have the room for a larger speaker then you can get a very big high quality sound with the Philharmonic Audio 1 ebony speaker and a Peachtree Nova.

http://philharmonicaudio.com/philharmonic1.html

If you have less room then I would suggest the Salk Soundbird speaker with a used McCormack 125 amp and a used Modwright preamp.

Bob