I purchased my GL1800 new in 2003 and now have 35,000+ miles on it.
Over-all, it's the finest motorcycle I've ever owned.
I bought a new 2007 Rocket III in 4/07 and now have ridden it a little over 6,000 miles.
For me, the Rocket is more fun to ride, just because of it's tremendous torque and horsepower.
Since replacing the Rocket's stock (stiff) rear shocks with Progressive Suspension 440 rear shocks (-1" length), my wife and I find the Rocket actually rides nicer than the 'Wing. Not that the 'Wing rides harshly, the Rocket just rides better.
Over-all, from a maximum comfort standpoint the Goldwing beats out the Rocket and extras like it's full fairing (to keep legs warm), excellent intercom, radio, large windscreen, etc. add to this. I also really appreciate all the lights on the back at night.
When it comes to handling, both bikes do a great job. The 'Wing handles quick transitions a bit better but the Rocket offers more ground clearance. Both bikes are surprisingly nimble, especially for their size.
If I had to choose between them, I'd keep the 'Wing just because it does everything so well although the power of the Rocket is very addicting

.
I'm glad I don't have to make that decision