mission valley though a word of warning STAY AWAY THE LAST WEEK/WEEKEND IN JULY!
Cause that's when comic-con hits town and everything goes crazy....starting w/ most hotels doubling their room prices to milk out of town attendees for every dime they've got
2. Joe C
There are dozens of moderately priced hotels in Hotel Circle. They are all close to Sea World, Mission Beach, Old Town, downtown, Balboa Park and the Zoo.
You will not find much in July under $100/night. If you found a place for $600 for a week, it's probably a good deal.
Be aware that July 23-27 is the Comic-Con convention. Hotel rates triple for the convention and just about every hotel within 50 miles is booked solid that week.
3. Mark S
Some of the downtown hotels ranging in price from about $100 to $200 include:
Gaslamp Plaza Suites, Hilton San Diego Gaslamp Quarter, and Courtyard San Diego Downtown
For a more extensive list you can check out: