I am from Philly and I'd be happy to let you know of tons of places but you'll have to narrow down where you're going exactly. Philly is both a big and small city in my opinion. You can get a hotel in a nice section of downtown (Old City, Rittenhouse Square, City Hall, etc) and be walking distance to great places.
A few cool bars: Standard Tap, Monk's Belgian Cafe, Moriarty's Restaurant and Irish Pub, Tattooed Mom, McGillin's Olde Ale House, The Irish Pub, Eulogy Belgian Tavern, City Tavern
Philly also has some great dive bars. Just walk in any corner bar. Sometimes you may be walking right out but when in Rome.....
There are also brew pubs at Triumph and Nodding Head Brewing
Food is great all over the city. Try Yelp.com to narrow down what you are looking for.
Be sure to get a soft pretzel and some "Wooder Ice" at some point.
Some great places to see: The Liberty Bell and The Constitution Center which is very close to the City Tavern. The Benjamin Franklin Institute (one of my favorite places in the city; I've been there about 20 times and it still love wondering around for hours). The Philadelphia Art Museum is a good one too but I've only been there a handful of times, still haven't seen it all, its big.
As far as Pat's or Geno's....I am Pat's. But Steve's is my favorite (not in/near center city) and Jim's is great also (South Philly). By all means, go to Pat's/Geno's, it is a really cool set up. They are across the street from one another and boast very different set ups. As an alternative to a cheese steak you can try Tony Lukes: fantastic Broccoli Rabe sandwich. Be careful when ordering from any cheese steak place. They can be a little grumpy working in front of a grill all day, especially late at night after dealing with patrons who are feeling no pain.
Not that I don't love my city because I do but there are some scum bags here. Be sure to cab it after dark.