Cathy's probably got better ideas as she actually lives in SF, but hey, I'll give it a shot.
Running in SF: Try the Presidio (nice trails), Golden Gate Park, or along the Wharf (by Crissy field). You can also run along the Golden Gate Bridge. There's a place to park pretty close to the start of the bridge (sorry, can't remember exact directions, I could drive there, but...) and then you can walk/run over the bridge. Along the beach is also nice. There's a trail (paved) alongside the beach (at least for a bit) or you could even run along the beach itself if you could deal with the sand. Everywhere can get very crowded so earlier is better.
Swimming in SF:
http://www.pacificmasters.org/general/plctoswim.shtml Try this website, scroll down to San Francisco. I don't know which ones are the best but the South End Rowing Club has an area where you can swim in the bay (known as Aquatic Park.) Either bring your wetsuit, or be prepared to get very cold.
Entertainment:
http://www.sfgate.com/ - Over on the left are links to entertainment. Not sure what you are interested in, but this will give you a good list of what's going on, possible places to eat, etc.
http://www.sanfranciscoonline.com/ - This site also had some cool stuff that you might want to check out.
The Exploratorium can be cool, especially if you go with a kid.
http://www.exploratorium.edu/ SFMOMA (Museum of Modern Art) has half-price admission on Thurs 6-9, if you're interested in art, they've got a great collection (I like some of it, and some could go in the trash for all I could care.)
http://www.sfmoma.org/ Have fun!
Shellee in CA