As you may know, Leah and I are moving overseas in February. First though, we're having a holiday in San Francisco for a week.
We chose San Francisco because we weren't particularly smitten with the places we could go via Asia (although Japan would have been really nice). That pretty much leaves going through the US or Australia, and there's no way we were going to go on a flight direct from Sydney for 23 hours. So, it was either San Francisco or Los Angeles, and San Francisco looked lovely. It's not the warmest place, but it's very compact and looks to be tourist friendly.
After booking our flights, we took a look at activities and accommodation. I can recommend the Fodor's San Francisco book for lists of things to do -- we were lucky enough to find the 2009 version at our library, and have consulted it pretty heavily.
I can also recommend Expedia -- so far, at least. We took a while to decide where to stay; the guide book was particularly helpful in recommending areas to stay, but the hotels it recommended were a bit out of our price range. Luckily Expedia lets you search individual suburbs. We eventually chose the Hotel Stratford (mostly because Expedia was having a sale on it the day we were looking :) )
There are a few websites that will help you deciding which place to stay at; Booking.com is a good resource, as is Trip Advisor. Trip Advisor especially seems to be quite good at filtering out the cruft. I've noticed that a lot of the reviews on other sites are brought down by somebody who likes to whinge, but Trip Advisor seems to have detailed reviews from seasoned travellers.
The bad side of things? Trying to work out where everything is so you can plan which days you're going to do your activities! I found out that Google Maps has a way of 'bookmarking' a location only after I put everything into Google Earth first. Still, at least I have a nifty KMZ file now, which I bet I can put into Google Maps anyway.