ucsd is a huge research school, so it's largely focused on the sciences. But I know a lot of other departments are well-respected. For example, our political science department (at the graduate level, anyway) consistently ranks in the top ten in the country.
Engineering, all the physical/natural sciences, psychology, economics, math, political science, cognitive science, international studies (relations) are all supposed to be great (in graduate rankings at least)
I have a whole bunch of friends who are going to SD for either bio or engr.
Political Science and International Studies are also on the rise. As a side note, UCSD has really good study abroad programs, especially if you're at ERC.