In looking for hotels on your Philly vacation, a couple of things really help:  a pool and free breakfast in the mornings to get them set-up for the day, and a suite layout for extra space and privacy for parents.  Always check recent reviews before booking.

 Suites Hotels: 

 Residence Inn Center City Philadelphia (1 East Penn Square) - right in the heart of CC Philly - Complimentary breakfast buffet and complimentary dinner 3x a week. No pool.

Embassy Suites Center City (1776 Benjamin Franklin Parkway) - Located near many museums and other attractions; others within short walking distance. Large suites.  Full breakfast included. Evening manager's special includes free drinks for parents and snacks.  Build-A-Bear Workshop kits are a must for kids. No Pool.

 Windsor Suites (1700 Benjamin Franklin Parkway)- just a block away from the Embassy Suites.  Rooftop pool. Continental Breakfast.

Non-Suites Hotels:

 Hilton Garden Inn Philadelphia (1100 Arch S) - indoor pool and hot tub - can get packages with breakfast included - nice junior suites as well for the family.

Sheraton Society Hill (1 Dock Street) - right in the historic district, has a really nice indoor rooftop pool with a kiddie splash pool for the little ones and a hot tub for the big people.  Skip the overpriced breakfast in the hotel restaurant and walk a couple of blocks to the South Street Diner - they have a great kids breakfast menu and excellent omlettes for Mom and Dad.

Hyatt Regency at Penn's Landing (201 S Columbus Blvd) - located right on Penn's Landing with great views - great indoor pool with views of the river.

Hampton Inn Philadelphia Convention Center (1301 Race Street) - deluxe continental breakfast is included (usually has one hot entree) - hotel also has a nice indoor pool and hot tub.

Doubletree Hotel Philadelphia (237 S Borad St) - located right along the Avenue of the Arts - nice indoor pool and hot tub - breakfast in the hotel is a great spread - but if you'd rather do ala carte elsewhere, check out the Marathon Grille two blocks away.

Omni Hotel Independence Park (401 Chestnut St) - location cannot be beat - right in the heart of the historic district.  Indoor pool and jacuzzi.

Wyndham (formerly Holiday Inn) Historic District (4th and Arch) - great location in the historic district - seasonal outdoor pool.  

Philadelphia Courtyard Marriott  (21 N Juniper St) - indoor pool and hot tub - check Marriott's website directly for rates - can sometimes get breakfast included with the room price.

Crowne Plaza Philadelphia (1801 Market St) - nice hotel in Philly's business district with a seasonal outdoor pool.

Four Seasons Philadelphia (1 Logan Square) - Your kids will get treated right here with a welcome gift and cookies and milk sent up to the room.  Beautiful indoor pool, huge hot tub.  If you can afford it, this is a great place to stay - they also do packages on their website that include breakfast.