WebDigger made me do it - for California at least. Here's what I could find this afternoon regarding emergency and non-emergency operational and security contacts in California.

In general, if there's an emergency, CALL 911. You might have to tell the 911 operator that there's a railroad involved, and possibly which one; they may or may not do anything with that. If the problem is specifically railroad-related, and isn't an emergency requiring public response, try one of the numbers below.

Many smaller railroads and most transit agencies don't have a “police” or similar number for the public. Call 911 if it's urgent, or call the office (regular business hours) or customer service (phone tree…) and let them know there's a problem. Nearly everybody these days has a web site you can get a phone number from.

Grade crossings: nearly all have DOT numbers – provide it when reporting a problem. Most grade crossings with gates/lights have a hotline phone number posted on the equipment shed for reporting problems; use that if available. Call 911 if there's a safety issue (i.e. most of the time with grade crossings).

FRA Grade Crossing Inventory System: [www.fra.dot.gov] might help if you have a tablet/laptop, have data service, and can't find a DOT number otherwise.

UP (http://www.up.com)
Police (urgent or suspicious-circumstances calls): 1-888-UPRRCOP (877-7267)
Rough, damaged, or obscured grade crossings in California (non-emergency): (916) 789-6114
Emergency grade crossing blockage or damage: 1-800-848-8715 or call the police number.

BNSF (http://www.bnsf.com)
Emergencies (including grade crossings), Report Trespassers or Criminal Activity: 1-800-832-5452
Supply Chain Security: 1-800-507-9227

Coaster (San Diego) (http://www.gonctd.com/coaster)
Call 911. For non-emergency grade crossing or signal problems call (800) 404-9464.

Caltrain (SF Peninsula) (http://www.caltrain.com)
Call 911. Caltrain Police: (877) SAF-RAIL ((877) 723-7245).

Amtrak (http://www.amtrak.com)
Call 911. Amtrak Police: 1-800-331-0008

BART (http://www.bart.gov)
Call 911. BART Police: 510-464-7000

Genesee & Wyoming N. Calif. Lines (CFNR, CORP, SJVRR) (http://www.gwrr.com/)
Call 911. Railroad emergency: (800) 800-2203

Genesee & Wyoming S. Calif. Lines (VCRR, SDIY, AZCA) (http://www.gwrr.com/)
Call 911. Railroad emergency: (866) 527-3499

Sacramento RT Light Rail (http://www.sacrt.com)
Call 911. Security: (916) 556-0275. Grade crossing problems: (916) 648-8433