SF Tourists.

The remodeled Cal Academy of Sciences is cool - get there early though as it gets crowded.  Haven't been to the new Exploratorium.

Another fun and cool outdoor thing to do this time of year is to go to the Marin Headlands (northside of GG bridge) and go to the top of Hawk Hill to check out the Fall hawk migration.  This is the peak time and you can see 200-1000 hawks/day of up to 10-20 species depending if you hit a good day.  Peak time is 1000-1500, bring binoculars, hats, etc.  It's pretty cool to spend some time sitting on the top of Hawk Hill overlooking SF and the GG watching 100s of wild hawks migrating past.  Shoot me PM if you want more info.

Do you like lighthouses?  It is near Hawk Hill, there are also a lot of WWll concrete bunkers where they had huge cannons to defend the SF bay.  There is enough in this area to explore all day and a bonus is that it is generally not crowded like the SF area is.  If the weather is clear you can get some spectacular pictures of the Golden Gate bridge and the City from this area, also when big ships head in you have a great view of them passing by.   
http://www.nps.gov/goga/pobo.htm

+3 on the exploratorium, even if you don't have kids.

if you can get them up early CHina town very early AM is nearly as cool as Tsukiji

Yeah dude, you are going to want to stay waaay away from the west end of golden gate park this weekend. Unless you want to see some amazing and free music.

There IS a decent Chinese restaurant in Chinatown; RG Lounge

 https://www.facebook.com/pages/RG-Lounge/46313958681

The remodeled Cal Academy of Sciences is cool - get there early though as it gets crowded.  Haven't been to the new Exploratorium.

Another fun and cool outdoor thing to do this time of year is to go to the Marin Headlands (northside of GG bridge) and go to the top of Hawk Hill to check out the Fall hawk migration.  This is the peak time and you can see 200-1000 hawks/day of up to 10-20 species depending if you hit a good day.  Peak time is 1000-1500, bring binoculars, hats, etc.  It's pretty cool to spend some time sitting on the top of Hawk Hill overlooking SF and the GG watching 100s of wild hawks migrating past.  Shoot me PM if you want more info.

Do you like lighthouses?  It is near Hawk Hill, there are also a lot of WWll concrete bunkers where they had huge cannons to defend the SF bay.  There is enough in this area to explore all day and a bonus is that it is generally not crowded like the SF area is.  If the weather is clear you can get some spectacular pictures of the Golden Gate bridge and the City from this area, also when big ships head in you have a great view of them passing by.   
http://www.nps.gov/goga/pobo.htm

Atavuss is right-on here.  Lots to explore in the Headlands.  In addition to the lighthouse and bunkers there are the old Nike missle sites from when the military owned the land prior to it being transferred to the NPS.  There is also the visitor center which gives good local history, the marine mammal center, alot of nice hiking trails, and Rodeo beach to hang out.  It's an amazing natural area so close to a major city. A picnic on top of Hawk Hill on a nice clear Fall day with the view and hawks is hard to beat.

I used to live a few blocks from chinatown ~10-12 years ago. The only place on grant worth eating at was Bow Hon.  Quality and service varied widely, the more white people in teh restaurant the worse it got.  Best bet was to go in, look around, and if more than one table full of non-Chinese people, leave and come back another day.

I Zod  very nice list!

Fort Point, I thought was cool, more so if there happens to be any reenactors there.  I was going to say Eddie Rickenbackers, but after searching for it, I found they got rid of the motorcycles, now it is just a pub.

Lots of great suggestions here. 

For Chinatown, take a walking tour... they'll show you some interesting places and the history behind them.  And look at the sidewalks, there're usually little bronze plaques imbedded that have a little history.  There's also the hole-in-the-wall fortune cookie "factory."  Not much to look at but buy a bag of cookies to munch on while you walk around.  I will second Ski Pro3's recommendation of RG Lounge.  Good food, done right (and it's clean).  I'll also back up Crash on his recommendation as to look inside the restaurants.  If the clientele matches the cuisine, it's usually good.  Especially in Chinatown, most shops have a dish they're known for... the rest of the menu is just OK.  I recommend Capital Restaurant's fried chicken.  TOTALLY AWESOME!  As for the shops in Chinatown, they're all tourist traps but fun to look around.  Building codes don't mean much so you can really get into some tight quarters and underground areas.

If you're on the west side of the City, Irving St, Noreiga St, and Clement St are great places to cruise for restaurants.  Lots of good restaurants out there.  Also, the Dim Sum bakeries are better (and cleaner) than in Chinatown.  Grab a couple of baked pork buns, shrimp balls, or pork balls and you're set for a tasty walking lunch.

I will recommend that you stay off Mission Street from 14th St to Cesar Chavez.  It's still rougher than it should be.  However, Valencia Street has lots of good restaurants but it's like Hipster heaven. 24th St is a great street between Potrero and Valencia (just don't linger around the young men congregating on the corners... they tend to get shot every now and then).  Most of the Taquerias are good... all the locals have their favorites.  But... for the best Pupusas, go to Balompie Cafe on 18th St.

If you're a military guy, you might want to stop by the Marine's Memorial Hotel.  They give discounts to service members based on rank and it's actually like a mini museam inside.

Stop by the Tonga Room at the Fairmont Hotel (thanks crash) as well.  It's one of the last great Tiki Bars.  They have thunder and rainshowers inside.

Lots to see and do and EAT.  The only other tips I recommend are bring a jacket (usually gets cooler after 4pm) and keep your iPhone stashed in your pocket.  The young kids (boys and girls) travel in packs, they snatch phones/ipads, run... and they are QUICK! 

Try all the food... best place in the world.

 

  Wife/GF might like the Rose garden

Great rec on Tonga Room. It's a blocksup the hill and across the street though, in the Fairmont.

Tonga Room is cool but I don't think that's his cup of tea. Definitely a cool place. http://www.tongaroom.com/494/menu

Now he will definitely fit in the Mission no problem.

Know your target species 

Maybe I wrong.....

Lots of great suggestions so far. A couple of other free things to do -- you can go up in the tower at the DeYoung Museum to get an overlook of the park and the western half of the city. If you check out Sutro Baths/Cliff House area, there's a great walk along land's End that gives great views of the GGB and the Marin Headlands. There's also the cable car museum on Nob Hill not far from Chinatown -- you get a good view of the inner workings of the system and how the cables are driven.

If you do go to the headlands, the Marine Mammal Center is also pretty cool to check out.

Enjoy!

Also, to keep the pan handlers off me, I speak German at them;
"I don't speak English.  Do you speak German?"

"Ich spreche kein Englisch . Sprechen Sie Deutsch?

(Only works if you are Caucasian...)

stay away from that filty, dirty place and go to Muirwoods in marin. the city is a nightmare on the wkends dood.