A couple of month ago when I found out I was going to Juneau for a few days, I made a post about where to eat, but didn't get much response. So now that I've been, I decided I should share my experiences.
We went to the South East Waffle House by the ferry docks the first morning we were in town. I got an egg-le (egg bagel sandwich). I got mine with swiss and ham. It was good, though the bagel wasn't crisp, but I overheard the two women behind the counter talking, and found out that they did not have a flat top, and that they microwaved eggs. If I hadn't known I would have been fine, but upon hearing this I suddenly had a harder time with the eggs. I'd stick with waffles here. My companions got waffles and were very happy. Good tea and coffee as well.
We they ventured into downtown Juneau. We had lunch at some food stands by the cruise ship docks. I went to a Filipino stand. Apparently Juneau has a large Filipino population. Who knew? I got a great pork bun, for 6 dollars. It was filling and very tasty. One of my friends went to a crepe stand and was very pleased (she is a vegetarian and she said they had the most options). My other friend went to Tracy's Crab Stand and got from crab bisque. She said it was great (and we later got a recommendation for it from a local) but it was very expensive, a dollar per ounce! I'd recommend these food stands for a cheap and fun lunch option.
We went by two bakeries, the Silver Bow Bakery and a Wild Sourdough Bakery. Both were fantastic! The Silver Bow specialized in bagels but everything we got was great (including hot chocolate, good for a chilly Juneau afternoon). This was a real nice local spot. The Wild Sourdough bakery had great bread and said that their started had been in use for something insane like 60 years. Both a great lunch or breakfast spots.
For dinner we went to Hot Bites! We had heard about Hot Bite's milkshakes and onion rings from approximately 5 locals by the end of our first day in Juneau. We were not disappointed! The milkshake was one of the best I've ever had (I got strawberry malt but everyone at my table enjoyed their flavors). I got a green chilli burger which was wonderful, but I envied the fish tacos one of my friends got.
I'd also recommend Alaskan Brewery's beers. I tried the Summer and the Amber. Both were wonderful! I wished I had had time to go on a brewery tour.
Hope that helps!