Craigslist and UPenn's off campus housing list are good resources to look at.
I would avoid the Temple main campus area. As for south philly, it really depends on where in south philly are you talking about. There are some parts of south philly that have really been developed and are pretty nice to live in. However, those parts of South Philly will have rents comparable to Center City prices. In general, the sections of South Philly that are closer to Center City are better than the ones further away from Center City. For University City, it will also depends on where you are looking at. If you live within the confines of the Penn campus and to some degree of Drexel's campus, it might be okay. If you live in the areas surrounding Penn or Drexel's campus, it will get more sketchy. The areas of University City that are decent to live at will have similiar prices as Center City prices.
Besides the SEPTA subway, there are two other train systems that service Center City. One is the SEPTA Regional Rail trains that runs into the suburbs and other parts of Philadelphia. Think of the Regional Rail trains as commuter rail to the suburbs. The other train system is the PATCO train lines which services areas of New Jersey near the Philadelphia area.
If you are willing to commute by public transportation, I would recommend neighborhoods such as Manayunk (which is about 20 minutes train ride on the Regional Rail train to Center City or by bus). There are some areas of East Falls (which is accessible by bus and Regional Rail) that might be okay as well. There are some areas of Northeast Philly that might be okay as well. For Northeast, I would focus on the upper Northeast Philly. These are the areas that the subway DOES NOT go to. I am referring to the areas of the Northeast Philly that can be reached by Regional Rail trains (such as Torresdale stop and Cornwall Heights stop on the R7 Regional Train line). Another nice area that you might want to consider include Chestnut Hill area, which is accessible by both bus and Regional Rail (30 minutes train ride). Roxborough, which is only accessible by bus, is a decent area as well. Roxborough is a blue collar family oriented area.
I noticed that you really avoided the Center City area. I would recommend you to look around in Center City area itself. Center City is a pretty big area that extends from Olde City to Art Musuem area (east to west). I would recommend staying south of Vine Street and north of South Street. There are some decent areas surrounding South Street but I would not venture too far south of that area. The only area north of Vine Street that I would recommend would be the Art Museum area.
I hope that this helps.