Innsbruck, Lake Garda, Lake Como, and Lake of Constance
 

We are contemplating a 4day car trip doing a loop listed above. Does this make sense logistically and is it worth seeing all these lakes?

Nice loop, but I would sub the Dolomites for Constance for a change of pace.

I agree. You still can wind up at the Lake Constance (Bodensee), but at its eastern end, in Lindau. From there easy drive to Fuessen Neuschwanstein or Munich.

Great, thank you. Any interesting places to stop along the way? Any suggestions for cute B&Bs at all three lakes?

We liked this hotel overlooking Lake Como: http://www.ilperlo.com/hotel-lake-como-bellagio/

There are tons of interesting places around the 3 lakes and in betweem. But in 4 days only, you can't even visit the most important sites. If you have more time, you can check:
Innsbruck city tour - Sterzing (visit) - Brixen (visit) - scenic Val Gardena - Bolzano/Bozen (historic city center, Oetzi Museum, historic Ritten railway), Lake Kaltern (vineyards, vinecellars, landscape) - Trento (visit), Riva sul Garda - Gardesana Orientale - Verona (Roman amphitheatre, medieval city center) - Sirmione del Garda (castle) - Bergamo (stunning medieval city center) - Lecco - Lake Como - Varenna - ferry - Bellagio - ferry - Tremezzo Villa Carlotta Botanical Gardens - Villa Olmo - Chiasso - Riva San Vitale Battisterio - Capolago cog railway to Monte Generoso view point - Melide Swissminiatur - Morcote church - Lugano (churches and medieval city center) - Bellinzona (3 castles, medieval city center) - Viamala Gorges - Chur (city and museums) - Heidiland - Werdenberg castle - Stoos - Appenzell (scenic vilage in scenic area) - St. Gallen (monastery and Unesco World heritage library) - Rorschach Lake Constance - Constance city center - Mainau Island - Arenenberg castle - Stein am Rhein historic city center and Hohenklingen castle - Rhine Falls - Schaffhausen (medieval city center and Munot castle) - Singen (Hohentwiel) - Ueberlingen - Salem Monastery - Unteruhldingen lake Dwellings - Meersburg castle - Friedrichshafen Zeppelin Museum - Lindau Island - Bregenz and Mount Pfaender - Neuschwanstein castle - Linderhof castle - Oberammergau - Ettal - Mount Zugspitze - Mittenwald - Innsbruck.

Michael, looks awesome. Neckervd, wow that's great info. We will try and stretch our time there a bit. I assume where you wrote visit, those are must see's, correct?