rvaccha,
Glad to read your post... I graduated from Wharton undergrad in '02, and made MANY, MANY, MANY trips back and forth between NY and Philadelphia. I did the Amtrak route. I even did the flying route (a $65.00 roundtrip on a Delta B767 purchased through Priceline).
But the CHEAPEST method of getting from JFK to Penn's campus -- while still maintaining a modicum of comfort -- involves the following:
1) NY Airport Service from JFK to Penn Station. The Subway is an even cheaper option, if you're willing to give up an hour or two of your life to a shuttle bus and then an interminable train ride through Queens and Brooklyn.
2) Once at Penn Station, purchase a NEW JERSEY TRANSIT ticket from New York to Philly. The one-way, peak cost is something like $16 nowadays (a big jump since my freshman year). The trip is about 2 1/2 hours, and involves a change of trains at Trenton (to a SEPTA commuter train), but the ride is bearable and ALWAYS populated by Penn kids shuttling back and forth to home.
3) Once at 30th Street Station, take a $5 cab ride or hop the free LUCY Shuttle to Penn's campus.
The only other cheaper ways, I think, involve unreliable Greyhound service or one of the mysterious Chinatown busses that go back and forth between the two cities for about $3 each way (or something like that).
Either way, I suggest SEPTA/NJT. Good luck, and best wishes to your brother for success at Penn!