Been to Lake Como a couple of times, including our honeymoon. It is one of the premier destinations in the world if you enjoy fantastic scenery and the history and architecture of Italy. We had lakeview apartment rentals in Menaggio and Tremezzo, and watching the white horse clouds/fog drift over the lake in the morning and then burn off by mid day while drinking an espresso on the patio deck is something you never forget. Walking along the waterfront and town of Menaggio was a regular excursion as well.
I second stslc's recommendation of boating to Bellagio and Varenna. We did these as separate day trips on the ferry system out of Menaggio, which was very reasonably priced and frequent. Spend a good part of a day walking around Bellagio, which is one of the most beautiful settings around, and dine near the lakeshore if you can. Varenna has some nice restaurants nestled into the hillside along a waterfront walkway perched up above the lake too.
We also enjoyed driving around the entire lake, stopping at various town centers of the little lakeside towns along the way, each with its own character and charm. There's a scenic plain on the north end too that leads into a smaller lake called Lago di Mezzola which feeds Lake Como.
We also enjoyed driving over to Lugano Switzerland, stopping at a random Inn for lunch (in either Carlazzo or Porlezza Italy on the east side of Lake Lugano, can't recall exactly), where we stumbled onto some of the best penne arrabiata I've ever had. Lugano is a more modern, busy city, but a nice side trip.
Also did longer side trips to lakes Maggiore, and Garda into the Dolomites, which are both very scenic. If you only have 3 days though, I'd focus on the small towns around Lake Como, and maybe a quick side trip to Lugano.