Call me the king of reviving old topics...
There are a number of places to foam in San Diego... but as mentioned, you'll have definate luck finding passenger services while the chance of shooting a freight is all but nonexistent unless you like and are good at night shots (and don't mind hanging out near the yards until 2 AM).
*The Passenger depot has near constant activity between the Coaster, Surfliner, and trolley. A Northbound Freight usually leaves the yard at 7:00 PM with a second one departing around 9-10 pm. The Escondido Local comes southbound around 10 - 11 PM either with a load of empties, or as light power (an SD and a Dash-9 are the current power assigned). they pick up loads at the BNSF yard near the convention center, then head north to either Old Town / Miramar, or Escondido. Southbound freights usually arrive 11 pm - 12am or after. The last northbound freight usually comes up between 4am - 6am. Occasionally a northbound and/or southbound BNSF will go through the station between 2-4 pm.
*SD Trolley is guaranteed except between the hours of 1a - 4a. at this time the SDIY locals come to life, running east-west between El Cajon and Downtown, and North-South between Downtown and Tijuana using the trolley's lines. because of that absolute 3 hour work window, all SDIY freights are nocturnal, but sit on a South Bay trolley platform around 2 AM and you can get a good night shot (have a couple pals just so you don't get mugged though).
*Lastly, the CZRY in the far east county operates freight between El Centro and Mexico via the Carrizo Gorge, usually using leased UP Geeps and SDs, but occasionally using their own restored SP geeps, or a set of daylight F7s. You'd have to contact them to see if there is a good time of day to get some photos. (Carrizo Gorge Railroad)
*Other ideas: upline stations (Old Town, Sorrento Valley, Encinitas, Poinsetta, etc), well known locations (Torrey Pines state beach, Del Mar Surf, San Elijo lagoon).
Good luck shooting Sd county's eclectic mix of passenger services.. hope you get to see a freight in there too!