I currently own an FZ-07. Traded my R3 in on it. Have also ridden an FZ6R and I didn't care for it. Haven't ridden a ST. R3 and FZ both great bikes but the perfect bike for me would be right between them!
I'm sure you really can't lose with any of those three choices - ST seems legendary based on reviews.
I like having the torque on demand in any gear the FZ has but not the brutal nature under acceleration where you have to be careful to not let the front wheel come up aggressively. It was nice to be able to wring out the R3 full throttle and not worry about it. I'm not interested in doing wheelies.
R3: More comfortable seat; just enough forward lean I had to make an effort sometimes to use core/grip tank to keep weight off my wrists, but not bad; great looking bike; fairings a pain doing maintenance; great price; got 60-62 mpg;REALLY nice instrument cluster, (best of any of the bikes I've ridden); very nice handling in medium to sweeper curves; but like the FZ with straight handlebars and torque better in the tighter stuff. S20 tires really transform the bike with more confidence in cornering and better ride feel going from the stock bias ply to radials - people who complain about suspension on R3 really need to change tires first - makes a big difference.
FZ: Pretty awesome on tight mountain roads - torque is nice for pulling through and out of the tight twisties and dealing with traffic/idiot drivers; seat sucks; instrument cluster bleh; I get only 3-4 mpg less fuel efficiency than the R3 with twice the engine/HP/Torque - that's pretty awesome, don't know how they did that; nice to have more standard tire sizes for more choices and the tires last longer. Seating position for me is perfect, with the exact amount of forward lean I like. Felt a little weird at first coming off the R3 but that went away almost immediately.
Now that there are lightly used R3s on the market for mid to high $3k range I think that would be best bang for the buck. If you buy new the delta between R3 and FZ is not that much and the FZ offers a lot more performance. If you live near the mountains the FZ will serve you better in the tight stuff. If you commute a lot, do a lot of HWY and/or sweeper type curves - R3 may be better choice for that. If you want to be a major hooligan - get the ST?
If I could go back and get my $3800 difference I paid on the FZ when I traded my R3 I wouldn't do the trade again. I'm hoping Yamaha will put something out between them like a FZ450 or FZ-05? Until then I'll keep riding the FZ7