We've stayed at the Courtyard Marriott Downtown which is right across the street from the city hall. When we booked, they were having buy one night, get one night for free, so it made the hotel very, very affordable for us.
Slightly outside the city (we had family living in Bala Cynwyd that we were visiting), we got a room at the Crown Plaza City West on City Ave. right off of 76. We got it through Hotwire and got a great rate. I forget the name of the road, but there's a road right next to it that takes you down to the Schuykill River and you can take it all the way into Philly... it's a very nice, scenic drive that avoids the highway congestion.
DH and I have stayed there too - it was nice, and relatively reasonable. We live nearby (about an hour away), and we were deliberately staying overnight in the city. We've also stayed at the Indepence/Independant Hotel - something like that. I liked that one too, and would probably try that again, but the night we stayed the street crowds seemed VERY loud - we had a hard time sleeping...
*IF* you should decide to go outside of Philly, another good area to look is along the R5 regional rail line - that way you can leave your car behind. Towns like Ardmore, Haverford, Bryn Mawr, Radnor*, and even King of Prussia or Valley Forge (a bit farther off the Main Line) probably have hotels. (*The Radnor Hotel is where I had my wedding 15 years ago - I think it's still getting good reviews - not sure of the pricing, though.) King of Prussia, Valley Forge and Devon seem to have some chain hotels that you'd be more familiar with. The R5 line is a commuter rail, so it's generally very clean/friendly, and it can drop you off at 30th Street Station or the Reading Terminal Market.
If you didn't mind a farther drive, and wanted to catch some of the battlefields, I live near Longwood Gardens and the Brandywine Battlefield, and can recommend some local hotels for you... Oh, and the plus to where I live is I'm halfway between Lancaster (Dutch Wonderland, Hershey, outlet shopping, a Train museum, Amish farms/corn maze in the fall) & Philly, in case you wanted to see more than the city.