Well, I'm a bit partial to PRS, so I say go that route, but only if you like how it feels, plays, and sounds. PRS guitars aren't for everybody, but I just so happen to love them. PRS guitars (with a few exceptions) have a very modern tone to them. In other words, if you plan on playing a lot of classic rock, you might want to look more into the Gibson route. Don't get me wrong though. I play every style under the sun on my Custom 22, and it pulls almost everything off very nicely.
I had been looking into getting one of the new SE singlecuts, but then I ran accross a Yamaha AES620. This is an amazing guitar for the price. It's also very versatile. It has a Seymour Duncan JB pickup at the bridge, which has plenty of output for all types of rock and metal. At the neck, it has a Yamaha designed PAF style pickup, which produces some very nice les paulish type tones.
I wouldn't limit myself to just those 3 brands. There are plenty of other brands out there that might offer you a better choice for what you're looking for.