Off the top of my head:
Colosseum: lines will be longest at this one. I would advise NOT doing it on free Sunday. If you book a 3-hour tour of the Vatican on Saturday morning (see my comment on that below), you'd have plenty of time to do this one in the afternoon. Pre-order tickets:
http://www.coopculture.it/en/the-colosseum.cfm
As your ticket also covers the Forum and Palatine, you could do one or both after the Colosseum OR come back in and do those on Free Sunday. They are less visited than the Colosseum so if you get there first thing in the morning, I'm guessing you'd stand a good chance of avoiding long entry lines.
Borghese: you have to have a reservation even for free Sundays as their normal crowd-control system (only 350 or so admitted for every reserved, 2-hour slot) still applies. Do this by phone, and as soon as possible as once reservations are gone, they're gone. 011 39 06 32810 from the U.S.
Vatican (museums and St. Peters): I would highly advise ordering tickets for the museums in advance, even though Feb. is low season. It just eliminates any chance of wasting time in a long ticket queue. You can do that here:
http://biglietteriamusei.vatican.va/musei/tickets/do
Even better may be to purchase a € 37, 3-hour combo tour of the museums/basilica through that same website. The beauty of these is that tours exit the Sistine directly into St Peters so you avoid standing in a second entry/security queue for the church. After your tour is finished, you can take as much time as you wish to wander the basilica on your own.
http://mv.vatican.va/3_EN/pages/z-Info/MV_Info_Servizi_Visite.html
Cinque Terre: February is off season for the CT, many hotels and restaurants will still be closed for winter, and the ferries will not be running. Trails will largely be closed as well. Weather will be iffy - it could be cold, windy, rainy or all three - but crowds will definitely be much lighter for all of these reasons.