I was in the same situation as you. You have to ask youself, what do you want to do with your bike. Long rides, commuting, weekend warrior, stunts, etc.
I considered a bunch of different bikes for my second bike. As you can tell from above, I had it narrowed down to 2. But I ending up with something else. I am sure people here will disagree with me on some of this but this is how I decided:
Suzuki GSX-R: Light, good looks, but too uncomfortable.
Ninja 600R: Comfortable, did not really like the looks.
Yam R6: I have never ridden one but I hear they are not very forgiving to mistakes. IMO Good looks, except for the front. I just can't get used to those head lights.
Yam 600R: Heavier, very comfortable, bad resale value (don't buy a new one unless you want to keep it for a long time.) Not as modern as the others, and not quite as quick.
Honda CBR F4i: Liked it alot. Good looks, comfortable, except for the rock hard seat.
So I had it narrowed down to a F4i and a Yam 600R. But because of what I mentioned above, I decided against the Yam. The reason I did not get a F4i is because of the seat (passenger seat too because my girlfriend rides with me alot). The 99-00 CBR's were more comfortable for me and my girl, less expensive, and faster then the Yam. But not as fast as the F4i.
The short of it is, get a bike that fits your needs. Sit on all of them to see what is comfortable to you and think about what kind of riding you plan on doing.