If I was buying again I would be looking for an oversize headtube and full carbon fork on the spec.
Modern bikes seem to allow for a wide range fitment, I have two road bikes different sizes but the bars, seat and pedals are in the same place on both.
Colour and styling is importnat to me I like a bike thats pleasing to look at.
Ride handling is a difficult one, I can usually discount a bike on a short test ride due to its angles or more likely because it has a short top tube(latest tricross for example).
The frame qualities I would look for are- a stiff non flexy bottom bracket and removal of that energy sapping road chatter you get at speed on bad road surfaces which is difficult to gauge on a short ride.
Also factor in for some new wheels(basic fulcrums or mavics) as the OE ones are invariably rubbish.
Having said all that the £999 giant defy alu sl was a the best bike for buck I spotted when doing the rounds recently.
Versatile too with well hidden mounts for racks and guards which you may not want now, but never say never.
A bit sportier is a the Allex sport also in aluminium(with some fancy welding) but with a full carbon fork and 105 for £1200 very light.
If you can beg borrow or steal a bit more cash then the new Cervellos look lovely but are around 2k.