We returned from the Norwegian Gem Western Mediterannean cruise and would like to share some tips for those intending to visit ports on their own. Firstly you will need to make an early start and plan carefully eg obtaining train schedules in advance.
Valetta (Malta) is easy to get to from the pier, but not well signposted. Turn right after getting off the ship until a sharp left turn (almost a U-turn) uphill, then look for stairs across the road for a short cut. Best to get exact directions.
Civitavecchia (for Rome) is far more easy - take the free shuttle from the ship to outside the port. Turn right following the waterfront for about 10 - 15 minutes (lots of other pedestrians will be lugging bags so just follow them). Look for big sign Civitavecchia (station) on the opposite side, slightly elevated road. The 8 euro fare includes all metro rides in Rome so it's a much better deal than the drop off and pick up service the ship does. St Peters (San Pietro) is four stops before the main Rome Termini station, so you can stop off on the way there or back switching to the metro. The ticket for Coliseum includes Palatine Hill as well.
Livorno (for Florence and Rome) is much more complicated. Firstly, shuttle bus (1 euro return) to the town, walk a couple of yards to the public bus (you have to buy your tickets from the tobacco shop) to the train station. Return fare is 13 euro to Florence, and you can get down in Pisa on the way. At Pisa, a public bus goes to the leaning tower, beware of teenage pickpockets on the bus coming back.
Villefrance (for Nice and Monte Carlo) - turn right after getting off the tender following the waterfront almost to the end of the shops. Cross the road and take stairs up to the station (you can see the railway line behind the shops). Take lots of coins to avoid a long wait in line at the ticket counter take lots of coins, as the ticket machines take only coins or credit cards (with PIN). Trains go south to Nice or north to Monte Carlo and are not that frequent.
Hope this is useful.