SFO is my home base, and I can vouch for it being one of the most delayed US airports. In order for SFO to function as scheduled, all 4 runways must be in use. However, due to the configuration of the runways, whenever there is low visibility (which is quite often) the airport shuts down to 2 runways, and in extreme cases, 1. The result is horrible: UA shuttle flights become a mess. Delays of up to 4 hours on flights to LAX, for example, are commonplace.
On one occasion, on a busy Sunday UA was so backed up on LAX flights that they found an old 747 at SFO to cram in all delayed LAX-bound passengers. Quite unusual.
There are plans at SFO to build new runways, but this involves building more landfill onto the bay (the only place to expand) and this has environmentalists worried. Interestingly enough, at OAK and SJC, the other main Bay Area airports, delays are not nearly as common, due to less traffic and better runway configuration.