The Amtrak Keystone Service, which runs from Harrisburg to New York via Philadelphia, stops in Lancaster (and also Elizabethtown and Mount Joy). It has 14 trips/day on weekdays and 8 trains/day on weekends in each direction and all trains stop in Philadelphia, Lancaster, and Elizabethtown (most but not all trains stop in Mount Joy). Lancaster Station is located at the north end of the city and is easy to get to via PA 72, and has inexpensive, paid parking (I believe it is $4/day). Elizabethtown is located at the west end of the town and has free, though limited, parking. In Philadelphia, Amtrak stops at 30th Street Station, which is just across the Schuylkill River from Center City. Depending on where you work in Philly, you could walk to work, or take any Center City-bound SEPTA Regional Rail train for free to either Suburban Station (near City Hall) or Market East, using your Amtrak ticket. Time-wise, one-way trips between Lancaster and Philadelphia take a little over an hour, while Mount Joy and Elizabethtown trips to/from Philadelphia are a little longer. Cost-wise, I think Lancaster-Philadelphia Amtrak tickets run about $14 one-way, but monthly passes are available and provide significant cost savings over the regular fare. I believe 10 ride passes offering some discount over the regular fare are also available.
Though I never commuted on a regular basis on Amtrak, when I lived in the Harrisburg area (up until 1 1/2 months ago), I used Amtrak on an occasional basis (every 1 1/2 to 2 months) to travel to/from Philadelphia and less often New York. IMO, it is the best way to go from Harrisburg or Lancaster to Center City Philadelphia; the travel times are faster than driving in rush hour conditions and you don't have to worry about traffic congestion or parking. In the approximately 20 times I used the Keystone Service, I only had a problem with a train running significantly late once, and that was when Amtrak was doing major track work on the corridor in 2006.
Here's a link to the current Amtrak Keystone Service schedule (which may change slightly in a few weeks):
http://www.amtrak.com/timetable/dec07/W10.pdf