I will second the Brew Dog tap room in Florence. I think that was the best beer experience we had. It's definitely worth checking out as they had some very unique stuff from Europe (all over, Scandinavian, etc). Also, Archea Brewery in Florence is supposed to be good. We didn't make it there, though. Mercato Centrale has a good little bar and excellent food options, but no A/C so pick the time of day you go wisely!
In Rome, there is a great little bottle shop near Campo de Fiori called Johnny's Off License. Good selection of Lazio region beer and they brew and sell some of their own. Also, I picked up a Cantillon Kriek from there so that was awesome. There's a Peroni beer house (Antica Birreria Peroni) in Rome that is supposed to be cool but we didn't make it there. Open Baladin, also near Campo de Fiori is worth checking out.
As for Cinque Terre, I recommend just sitting back and drinking Peroni or Birra Moretti and enjoying the views while taking it slow. Not much beer to be had around there.
We didn't stay in Siena but did three nights in just outside Montepulciano and I would definitely focus on the wines in that region. Brunellos, Nobiles, etc. All so good and reasonably priced.