I've had a testride of the new Transalp 700 (twice) and also the V-strom, along with the Versys - see my post on this forum (V-curious).
I'm a big fan of Transalps and Hondas in general and was very surprised when I came to the conclusion that the V-storm was the best bike of the three - I only took a testride of the V-strom by chance.
The Honda definately has the edge offroad, feeling narrower and it felt a bit more balanced than the V-strom - and has better tyres and wire wheels.
I've not ridden the new BMW F650, but did have a seat on one at a motorcycle show. It's quite a nice bike but I didn't feel it had the build quality of the Honda or the presence of the V-strom. I'm not a huge fan of BMW and their build quality isn't what it was - according to various sources on the internet.
For hauling luggage there's only one winner, it has to be the V-strom, it got by far the best fairing, although the standard screen isn't so good. It's also the most fun to ride.
In terms of engine performance I don't know about the BMW, but the V-strom definately has a better engine than the Honda, even though it has less CC.
In summary, I'd probably by the V-strom, but wouldn't be unhappy with the Transalp. I wouldn't buy the BMW, although the F800GS is another question
if I was rich!