I thought I'd throw in any thoughts I have on the matter in case you are having trouble deciding.
Hands down my favorite hotel is the Marriott Hotel & Marina. I've been attending Comic Con since I was 2 years old (except for when I was 16 and got detained at the airport coming back from a summer program in Ireland cause they thought I was a runaway from Reno...no joke...ended up missing the only day of the convention I was gonna get to see which meant missing crushes Jason Lee & Ben Affleck who were appearing for some reason) and have stayed at the Marriott every year, except for one year where there was a mix up and we had to stay at the Omni. The rooms and decor of the hotel are classic & distinguished, the pool area is amazing and giant complete with a Tiki Bar that I may or may not frequent on Wednesday & Sunday, great restaurants, adjacent to the convention center (with secret easy ways to get over there) plus TONS of professionals stay there and it's right next to Seaport Village, which is nice and relaxing. A favorite Marriott memory is seeing Stan Lee chilling in the lobby at 1am in his robe. EruiteChick felt compelled to say "Lookin Good, Hef", referencing his cameo in Iron Man, and he said "Thanks!" It was glorious.
If you are looking for a more...hip? experience, try Hotel Solamar. It's more expensive. Far more expensive. This is where the crew from Entertainment Weekly stayed last year and threw their huge party. Cool looking rooms. Lots of professionals stay here as well, just...a different brand of professional? Less Stan Lee for the whole convention, more Matthew Fox for one night. The pool area is awesome, I think...the EW party resulted in a lot of drunk for me...and some of the rooms open up directly to the pool, like cabanas. Modern, stylish decor and while farish from the convention center, is close to the Gaslamp Quarter, where you will no doubt find press, publicists and fans alike getting wasted every night of the week. PS has anyone else tried that new Australian beer place? I'm a fan.
As for the Omni, the rooms were smaller than I was used to and the pool was wholly unimpressive, but it was right across the street from Hall H, so if you are the type of person who prefers proximity to the Hall H line over anything else, the Omni may be the way to go. Plus it's next to the entrance to Gaslamp. Location wise, it's pretty amazing.
The owner of the Hyatt gave $125,000 to Prop 8, so I know a lot of people have and are continuing to boycott them. It's a pretty hotel, but kind of far from the Convention Center, in my opinion.
I've never actually been in the Hilton Gaslamp or the Hilton Bayfront, but both locations are great and I think a lot of press professionals opt for the Hilton Gaslamp. Hmm...I may have gone inside the Gaslamp one during the Accepted party actually. We somehow talked our way into the VIP section and accidentally left david and Nick Frost alone together without any buffers and they were forced to talk about the weather. Haha, good times.
Finally, if you are crazy rich and care more about running into young celebs in the hotel bar, try the W San Diego.
Anyone have anything else to throw in about the Comic Con hotels? Clearly I only know one of them pretty well, haha.