A lot of places in Europe that I have fond memories of are lakes. Germany's Tegernsee and Austria's Worthersee, and Switzerland's Vierwaldstaettersee (Lake Lucerne) come to mind as beautiful places worthy of spending time in, as well as the Italian lakes. If had to pick a couple I might do Tegernsee in Germany and Lake Lucerne. Tegernsee has a nice tidy feel to it, and I walked around the entire circumference of it 33 years ago (crazy things we do when we are younger) in one exhausting morning. Lake Lucerne has such a beauty to it, but also the nice town of Lucerne to go with it. Pretty magical in my book.
I have a few.....Slovenia's Lake Bled, visited a year ago last May and more recently, Lake Ohrid (Macedonia) this past October. Oh, and Lake(s) Maggiore and Orta in Italy.
I loved Lake Lucerne also, it's so beautiful. I also really enjoyed Lac d'Annecy (France), Lac Leman (Lake Geneva, especially the area around Montreux), Worthersee (Austria) and both Lake Maggiore and Como (Italy). In my book you can't go wrong with a few days on, or near, a nice lake and I always try to incorporate that in my trips. There's nothing more relaxing than taking a short cruise on a scenically situated lake, or a lake ferry around to different villages on a lake.
The Bodensee. On a sunny day, the view from the harbor of Lindau south to the Alps could not be more breathtaking. For such a lake, the water is also relatively clear, and it makes for excellent swimming in the summer.
I probably would have enjoyed Austria's Neusiedler See more, but the weather didn't cooperate during my visit.
I've only driven by, but the view of Lac Lehman from Montreux is pretty amazing.
How about Lake Como on the Italian/Swiss border? Or, the very popular Lago di Garda just west of Verona, Italy?
Lago di Garda and Lake Bled easily come to mind.
My favorite lake - Morskie Oko (the Sea Eye) in Poland's High Tatra mountains right under the tallest mountain of Poland - Rysy. Unfortunately swimming there is prohibited but anyway it would be only for very brave, it's icy cold even in summer. The lake is not only sea eye but also eye candy.