We just had our Honey-moon in Italy.
In Rome, we used a tour company canned DarkRome (darkrome.com). Their tours in Rome were great. As long as you can afford to pay for the tours, they beat waiting in line to go in solo, and the extra information you get from a tour guide is well worth it. Waits in some of these places can be hours long, so a tour can be worth the price simply in the time you save. The same company offers tours in Florence, however I wouldn't recommend them there. Though you will probably want to be part of a tour in order to skip the ridiculously long lines at the Ufetzi and the Accademia there may be some cheaper options. Also in Florence, they aren't so much skip the lines, but stand in slightly shorter lines.
In Rome, take at least one day to wander through the city and see all the major free places. Pantheon, Trevi Fountain, Spanish Steps, Wedding Cake etc. etc. are all free places you can easily walk between. There are so many ancient structures and ruins available that don't need tours, but are just sitting there open for everybody to see.
Two of our favorite restaurants in Rome were Colline Emiliane and Ristorante Cesarina. Collinne Emiliane is widly regarded as the best pasta in Rome. If you want to go you HAVE to make a reservation. We made ours in the morning for an evening meal, so it doesn't have to be super far in advance. But don't show up at dinner time thinking you will get in. Both of these places are expensive if you get the full 3 course meal with desert. That really is a lot of food, but well worth it at these restaurants. In general though, 1 appetizer, 1 pasta, and 1 main course split between 2 people is more than enough. Check the side streets for local pizza stores. These places make roman style pizza's that the locals eat. Less than 10 euro's for 2 people, and some absolutely delicious pizza.
In Rome, one should NEVER want for water. Pretty much all the water you see flowing is coming directly from the aqueducts and is some of the best water you will find to drink. Buy one bottle to carry around, and refill at these fountains. Romans call them "little noses". The look kinda like fire hydrants that have a spigot on them that looks like a nose. You will greatly miss this free access to great water in other cities, so use it while you can! Here is a picture:
http://www.flickr.com/photos/brady-pics/5788463610/
The best gelato in Italy is in Florence, at a place called Gelato dei Neri. Best pizza we had was also in Florence, at a local hole in the wall pizza place. Doesn't really have a name. It's on Via Giuseppe Verdi at the corner of Via dei Pandolfini. It is basically a tiny stand barely built into the building. We were in Florence for a celebration called White Night. Every single local in the city and surrounding areas comes out and packs the city. Every street and piazza in the city is full of people. These two places were absolutely packed with locals, so we went to both and were quite pleased.