We went last October half-term - really fab. What to do depends to some extent on the ages of your DC (if you have any). Our DD was 13 and one of the best things we did was - having watched some of DH's 'great lecture' dvd series on architecture - walking from the Baths of Caracalla, via the Pons Fabricus through to the Pantheon - appreciating all the barrel vaults and relieving arches. 
The best day of all was at Ostia - its an easy train ride which is within the limits of the travel pass! Surprisingly not crowded.
If you're going soon, temperatures should be pleasant for walking, we didn't really need coats just umbrellas a couple of days. Oh, and did someone mention comfy shoes? 
DH found some nice trattorias using a Lonely Planet guide on his phone, so I'd recommend you get that.
We got the roma pass to avoid the long queues at a couple of places esp the Colosseum (best on a sunday, the area is pedestrianized then), and if you want to avoid a mega queue for the Vatican museum there's a tourist office up at the Catel Sant'Angelo (which we also enjoyed) where you can pre-book.
We actually didn't bother going into St Peter's, DH and I had been before and found it peculiarly lacking in atmosphere relative to English cathedrals - that may just be us though!
And then there are so many other museums, some of which are very quiet because so many people just do the Colosseum/Vatican - e.g we really liked [http://en.wikipedia.org/wiki/National_Etruscan_Museum the Etruscan]] museum.