weasel
Eradicator
One more CB1 for the price.

Best really depends on you and what you define as most important. There are several fantastic choices.
The Street Fighter is certainly sexy and insanely fast with fantastic components. The ergos are a bit odd with high foot pegs and a pretty long reach to the bars for an upright bike. The price is pretty high.
The old Tuono (gen2) has everything. It's simply good at everything. You can find them for great prices. If you want something a bit exotic and relatively inexpensive, go with a Tuono. It gets poor fuel mileage, so if you plan on commuting regularly or sport tour with it, keep this in mind.
The Z1000 is probably the best bang for the buck. The engine is reportedly a bit buzzy, but the bike is fast and stable and unique in looks and won't make you go broke.
The KTM Super Duke is a lot like a Tuono; slightly less power but maybe slightly improved handling. Also like the Tuono it doesn't get great mileage.
The FZ1 is absolutely a contender, but the gen2 seemed to be a step backwards. Given the other tremendous choices out there, you probably need to be a dyed in the wool Yamaha guy to go this route.
The Speed Triple is a fantastic choice. It doesn't turn quite as fast as the others (execpt the FZ1), but has a very unique and extraordinary engine. The triple really is the best of both worlds (v2 and i4). The bike unique, has a gem of an engine and a lot of aftermarket support.
If you don't need to eat up a lot of highway miles, look at the Street Triple R. It has EVERYTHING; great handling, fantastic engine, after market support, some exclusivity. Really, the only thing the Street Triple R wouldn't EXCEL at is long trips (light weight and buzzy engine at highway speeds). Other than that, I think the Street Triple R may be the best bet.
Then there's the Brutale. The bike exudes sex. I LOVE the Brutale. They can be a bit temperamental with a small dealer network, but the bike's sex appeal and exhaust note make up for it.
Wish I knew more about the Honda. Could be the best bet. Haven't seen one, btu the reviews say it's great and it is certainly a great looking bike.
Like you, I'm really a naked bike fan. After owning an FZ1 and a couple of Tuonos I have a Speed Triple. They were all great bikes. I like the chassis on the Tuono the best and the engine on the Speed Triple the best. I commute close to 100 miles a day (round trip) to work. So, I opted for the Speed Triple. If my ocmmute was a bit shorter or had less highway I'd have gone for the the Street Triple R.
Good luck.
Since im biased, for a street ridden bike, I'd go 2nd Gen tuono again. Every year I get the urge to sell it and get something new, but after a few weeks, I dont want to sell it anymore.
I'd wait for the v4 version to come out and pick up a 2nd gen factory tuono with tasty bits for cheap. Then put gas in it and wheelie to your fav twisty destination.
Can you still get parts for those?

Speed Triple! Street Triple R gives you some trick suspension and brake bits but you can't turn down the torque of a 1050cc triple.
Really? Whats the deal? So if a dealer has a new 2007 it's now $7,499?With the new v4 Tuono coming out soon, Aprilia just announced a promo offer on all leftover Tuono 1000Rs at the dealers.... new bikes for $7,499![]()

With the new v4 Tuono coming out soon, Aprilia just announced a promo offer on all leftover Tuono 1000Rs at the dealers.... new bikes for $7,499![]()