Either/both?

I have never visited Annecy but I can say that Colmar was absolutely beautiful and one of the most pleasant surprises of many trips. We went to Colmar specifically to see the Isenheim Altarpiece. I had no idea how lovely the town itself was and we really enjoyed our stay. We had rented a car and drove to a few of the beautiful villages near the town and included a stop at the Chateau du Haut Koenigsbourg. It was easy driving and short distances between sights so no hassles. We spent 3 nights and had a wonderful time. Alsatian dishes were flavorful, hearty and a new experience. Our B&B has closed, which would be the only con. Good luck and safe travels.

As with Denny, my wife and I have not visited Annecy, but stayed in Colmar: 4 nights in 2017. It was a wonderful experience, and we rented a car one day to visit other towns. Our trip report is posted in the forum, with a link to the excellently-located apartment ("Studio Romantic") Trip report: https://community.ricksteves.com/travel-forum/trip-reports/alsace-france-colmar-and-villages-bacharach-germany-sep-2017

Both towns have charming historic architecture. I agree that the altarpiece is wonderful (and I am not at all religious); I enjoyed the Unterlinden Museum a lot. In my experience (second half of June 2017) both Colmar and Annecy get very heavy tourist traffic, though I don't remember really significant crowding inside the museum in Colmar. The sidewalks in the historic district of Annecy were particularly packed, though I walked along the lake for quite a while and saw very few people. I'm more tolerant of crowded sidewalks than the average tourist, but I've seen a few negative comments about how "touristy" Colmar is on this forum, and I found the historic center of Annecy to be worse. I think we just have fewer people who've been to Annecy recently. I say this not to discourage you (having enjoyed my visits to both places), but so you are mentally prepared to be one of many visitors.

One other warning: Annecy is near the Alps but not in them. If this turns out to be a (Northern Hemisphere) summer trip, be sure you have air-conditioned lodgings in whichever town you choose. It was miserably hot at the time of my visit to Annecy. You can take a look at actual, historical, day-by-day weather statistics on the website timeanddate.com. I see that I managed to arrive at the beginning of five 90F days; such luck I had--but then again, 2019 would have been worse.

Edited to add: As to which to visit, I preferred Colmar by a considerable margin. The historic area seemed larger, the museum was a substantial plus for me, and it wasn't so blasted hot. But Annecy has the lake, which would be a big positive factor for many visitors; I enjoyed the boat ride I took. They are very different towns, so I don't think visiting both would feel repetitive. The little Alsatian wine villages are nice; you'll need to research transportation options for those unless you decide to rent a car for a day or two. There are some buses, but visiting more than one of the small places on a single day will probably be a challenge.

We've been to both and also preferred Colmar. Larger historic area and a tremendous museum. They are two very different cities and Annecy's biggest draw is the lake where one can take a very interesting boat ride. My two euros worth is do them both.

Lynn,

I’ve not visited Colmar yet, but my daughter and I enjoyed our visit to Annecy a few years ago. We were there at the very end of May and I don’t recall any crowds.

Annecy was our second destination after having spent a few days in Chamonix.

Annecy is very picturesque; you have the beautiful crystal clear lake with the spectacular alps in the background, and canals running throughout the old town with colorful flowers everywhere.

We enjoyed walking around the town, taking a bus to a nearby lakeside village and just soaking the atmosphere of this charming place.
We also experienced 2 market days where we bought some tasty goodies!

Make sure you go to Glacier des Alpes for the best gelato/ice cream in Annecy!

I've been to both towns multiple times and I would recommend Colmar over Annecy.

The approach to Annecy can be absolutely (and time-suckingly) gridlocked in the summer and during their film festival. The town is certainly nice enough, scenic in places with the canals and historic architecture, and if you haven't seen many alpine or subalpine lakes it's definitely worth a visit, but in my view it was not especially remarkable.

Colmar, on the other hand, is, and it's convenient to get from there to many other picturesque towns and villages nearby.

My first question is: what time of year? If high summer they will both be crowded, in the off-season (such that it is) of spring and fall, the crowds will be a little less but both will still be lovely. The earlier in the spring or later in the fall, I would suggest Annecy for likely better weather. It also depends on your travel interests. If you like scenery and outdoor pursuits Annecy is nice, especially if you have time for a day trip to Chamonix or other Alpine area. The lake is beautiful and you can take boat rides, you can bike or walk around much of it, the views of the mountains from the lake are beautiful. If you're more into museums, cities, or wine country, then Colmar might be preferable. You can rent a car (if you won't already have one) and drive the wine route to see the small villages and you can day trip to Strasbourg - which is great also.

I spent 2 nights in each a few years ago and I'd be hard pressed to name a favorite between them. I didn't have a car but, since I'm not into wine tasting and visiting vineyards, I was fine without one. I did boat tour around the lake in Annecy, took long walks on the promenades around the lake, hung out in the old center and enjoyed their fantastic weekly market along the canals. In Colmar I loved the Unterlinden museum and also walked around the canals there. I took a day trip to Strasbourg (on a rainy day) and loved the cathedral there and just walking around the old town area.

hey hey halls19
haven't been to colmar but spent 7 days in annecy last september 2019. we really liked it's small time feel, gorgeous mountain views and lake annecy, many villages around the lake to visit, the canals "little venice of france", shops, cafes, marketplace within the village on fridays and sundays, take a boat ride, ride a bike on the trails and promenade of lake. sitting down to people watch "free entertainment" at street corners
blogforfrance.com/annecy
annecycitytour.fr shuttle van for a intro to city
frenchmoments.eu/annecy
flavourandsavour.com/annecy
larotisseriedethiou.fr we sat outside and had their set menu for fondue and wine. it was great
al vesuvio 13 rue de i'ile for pizza and calzones with wine, yummy. sitting outside. people watching and talking with our hands with a group of women from italy & germany. good times
creperie ti mad at 21 rue royale for sweet or savory crepes
ferme de la charbonniere is a working dairy farm serving lunch with see thru glass floors to watch the cows below. under restauration is the set menu. they bring like a small pizza oven to your table that melts the cheese to scrape on bread and potatoes. very good and interesting.
brasserie saint charles at 46 rue du parmelan, near our apt had the best homemade beef stroganoff as a special on the menu
took a private taxi 4-5 hour tour with gaelle of taxi-massingy.com (read her blog) to villages around the lake and that's when we had the farm lunch. saw chateau de menthon, which disney visited and brought vision back for snow white's castle at disneyland, stopped at col de la forclaz village to watch the hang gliders soar right above you and over the lake, green pastures listening to cowbells on the cows grazing up the hills. second saturday of october is "descente des alpages". annual town festival to bring the animals back down from countryside for winter. they are decorated, music, local artist crafts, food, locals dressed up.
basillica church that the pope has said mass there, the chateau in the town
la cure gourmande at 1 rue de la paix. local french candy, bisquits, cookies in gorgeous french theme tin boxes. bought a few souvenirs.
booking.com or tripadvisor.com for hotels, i would stay in or close to the village
annecy-hibiscus-apartments.com and near the train station
this is my own opinion, everyone has different likes and dislikes. up to you to decide what you're looking for, maybe you can stay in both places. it is very pretty area of france. hope this gives you some ideas. enjoy
aloha

Hi, Princess gave you a lot of good detail, so I will make this short. We also liked Annecy much better than Colmar. Here’s my trip reports with our hotels, etc. Annecy is at the beginning of the first one. Colmar is towards the end of the second one.

https://community.ricksteves.com/travel-forum/trip-reports/3-weeks-in-italy-france-french-locations

https://community.ricksteves.com/travel-forum/trip-reports/our-combined-solo-couple-vacation-in-france-2019

For me Annecy was a very pretty city on a lake with a fairly tiny quaint old center. I liked it for what I did, a day stop between Lyon and Chamonix, for a stroll and lunch. I didn't really wish I had spent more time there. I might have liked a bike ride around the lake? There also a small castle museum overlooking the lake you can visit.

I enjoyed Colmar more. For me it's a place to spend two or three nights (not including all of Alsace). More to see and do. More dining choices. Unterlinden is a top museum. The old center is beautiful and vibrant. If a castle is a big draw, you probably want to go to Château du Haut-Kœnigsbourg, one of the best, a car ride from Colmar. With more time you can visit an idyllic town or two on the wine route. Each one is prettier and more quaint than the last.

If I have to choose, definitely Colmar.