Well, I think you'll find more than you think with Google , but here are some things I liked:

Budapest - go to a butcher shop for lunch. Very cheap, good lunches. You can find a few in or near the tourist areas, but from what I saw it's more of a locals thing than touristy. A restaurant that I enjoyed is Rosenstein. It's a family-owned Jewish restaurant near the train station. The roasted goose was fantastic. While the ruin bars are both popular and touristy, it's worth visiting at least one while in Budapest. Walk up the hill to the castle rather than taking the funicular. It's a really nice walk with great views, and there will be very few people along the way, as compared to the long line below.

Vienna - Try any of the small sausage stands throughout the city. For dinner, one of my go-to places is Puerstner, for Schnitzel and potato salad. It's a few blocks from the Marriott. There are also a number of small cafes and restaurants in the Spittelberg area. I can't remember any names but it's an area worth visiting and trying for dinner. I wish I could recommend a good bar in Vienna, but for some reason I still need to find one myself! Also, on a side street off Stephenplatz, there's a small lunch place called Trzesniewski. Basically, they have trays of small open face sandwiches and mini-beers, all for 1-2 Euros each. Kind of like getting cicchetti in Venice. Great place for a light lunch or snack.

Munich isn't my area of expertise, so I'll let others add to my thoughts and comment on Munich. If I think of anything else (better!) I'll add to the list.