Megabus takes you from the Bay Area to LA and you can then take Amtrak to go to SD. Great deals on Megabus
Based on a recent forum posting it appears Megabus has returned to the Callifornia market. The posting referred to the SF/LA route, but I've got to think they probably also do LA/SD. Thus I think an SF to SD is probably possible.
That's all I can say right now, will try to check their website when I'm at a computer and not my phone. (Actually expect someone else to chime in before that . . . .)
Hope this helps,
Before Megabus, the cheap bus from SF to LA was the one my friends call "the Vietnamese bus." Maybe Amtrak between LA and SD, or ask on the LA forum if they know of any other options.
I recommend traveling on Amtrak the entire way if you have the time. The scenery and ride are much more enjoyable, assuming you stick with the Coast Starlight and Pacific Surfliner trains, but there is more time investment and a higher cost.
Megabus is the best CHEAP option between SF and LA. Buses alternate between San Jose and Oakland en route. There is no scenery to be had along the way, so you might as well take the overnight trip if you can sleep in a reclining seat.
To travel between LA and SD, I recommend Amtrak. It is more expensive than Greyhound/Crucero, but the ride is much better. Megabus does not run to San Diego. (It did in the past, but that is a different story!)
You can also take Metrolink and Coaster trains between LA and SD (via transfer in Oceanside), but the extra hassle is not worth saving a few bucks compared to just riding Amtrak.
Are the Starlight and Surfliner the only trains to do this route, are there any more basic trains? (l had a quick look to no avail )
www.amtrak.com -- what you see is what you get -- just those 2 trains. Is there a specific reason you are not wanting to fly ? The bus does not take the scenic route, one of the train does. If you have time, a nice train journey from Seattle to San Diego would be fun IMHO and you can then hop over, across the border.Edited: 6:57 pm, December 12, 2012
I'm flying into SF and after that just weighing out my options
Both Virgin and Southwest airlines have mid week flights from SFO to SAN starting at $59
But I'm stopping off in LA for a few days
Even easier. SFO to LAX has greater frequency and probably a bit cheaper. While LAX has the frequency of flights (and they are cheaper) you can also check Burbank, Long Beach and Orange County depending upon where in the LA area you're headed. Flight time = about an hour.
Then you can take the train to SD.