Here is the number for BART police in case you encounter any questionable characters while on BART today. BART POLICE: 877.679.7000
(UPDATED) After a brief exchange with Scott Marshall of Contra Costa Times on 5/1 regarding what best to do in these situations, he recommends the following:
Directly call police communications center, 510-464-7000, but the best way to get help quick is to use the intercom phone on the train.
Just talked with Zone 2's Sgt. Barry Williams. He says you're going to get a much quicker response by using BART's intercom system. You have to decide if it's safe to move to another car. But if you can and pick up the intercom, you go directly to the train operator and you're in contact with the police in seconds.
Describe the people, the behavior, tell them what train you're on and which direction you're traveling. They'll stop the train and investigate. If they can't get to you, they routinely call a local agency (Orinda police, Oakland police, and so forth), who are more than willing to assist another agency (they train for that).
If you call 911, then your call goes directly to the Highway Patrol's Golden Gate Division dispatch center in Vallejo, and then they transfer you to a BART police communications center.