Best $3,000 speaker/amp combo?

At the risk of effectively saying, "you should buy what I have," I will say that my office system, though in a slightly smaller room, makes really nice music. Naim NAIT 5i with Totem Model 1 signatures. Your budget is sufficient to replicate this system if you buy used on the 'Gon.

Happy Listening.

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!