A near conflict occurred when traffic departing from Runway 28 and Runway 1 at SFO turned toward one another because the clearance issued to the Runway 28 traffic was confused and/or not updated.

Narrative

Aircraft X; a B757; departing SFO Runway 28 westbound. On the flight plan he had filed KSFO.CUIT2. SAC.J65.PMD but the preferential routing was +KSFO.PORTE3.WAGES..PMD+; shown on the flight progress strip. Aircraft X departed Runway 28 and at about 2;200 FT appeared to start a right turn (which would have been correct to fly the CUIT departure. I immediately turned him left heading 270 and I believe I said for traffic. He seemed confused and questioned the turn so was a little slow in reacting. In the meantime Aircraft Y; an E120 departed Runway 1L on a EUGEN5 departure. The CI1 (Coordinator) called SFO Tower to give them a 'heads up' on Aircraft X and they gave Aircraft Y a right turn to a 010 heading. The separation was about four miles at that point (three required since Aircraft Y was not directly behind Aircraft X) and increasing due to the headings assigned. I had to wait a little to turn Aircraft Y back to the EUGEN departure to get the required five miles for an E120 behind a B757 as the departures come off different runways but eventually follow the same general route. I then explained to Aircraft X that he should have been on the PORTE route which would have been a 280 heading off Runway 28. He seemed concerned that maybe there would be a 'problem' to which I said; 'No we kept the required separation. I did explain that I saw he had filed the CUIT but the preferential (PORTE) should have been flown. I then gave him vectors to PMD and figuring 'no harm; no foul' I went on working the session. Later the OM came to the area and said the Aircraft Y pilot was on the phone concerned about the operation and the quick turn the Tower had given from a 350 to a 010 heading right before the frequency change. He wondered if there was a separation problem. I told the OM I was sure that was not an issue. What may be an issue though is in this ACARS environment this is not the first time I have seen something like this. In the 'old days' Clearance Delivery could clarify and make sure proper routing's were issued when a filed route was so completely different from the PDR. What is the procedure for transmitting and ensuring the proper receipt of a clearance these days? The situation on first look didn't seem that bad but; had I not caught it right away and CI1 and the SFO Local reacted as they did; it may have become a dangerous situation. There needs to be a way to ensure that a complete understanding of the route is received by the pilot.