I use this trick. Basically, Microwaves cook from the top, and heat needs time to go down. Additionally, microwaves can put a lot of power into the food, which can burn bits while keeping other bits stone cold. The only way around this is to reduce the power and cook for longer. Mixing as other people have noted is also somewhat effective.

Basically if you make a microwave oven take as long as a regular oven, it'll cook the food more evenly.