If you actually think about it, most wishes might seem like they're good, but if you take a look at some the consequences or the means to accomplish the wish, it might not be so good afterall.
For example, say you wished for all diseases to be cured infinitely. That might lead to overpopulation, and greater world hunger, etc. Or say you wished for world peace or to end world hunger. One could say that could be accomplished by eradicating the human race.
With that in mind, here would be my three wishes:
1. Pseudo-omniscience - the knowledge would be gained only as wanted. Knowing everything all at once might drive you mad, and there might be things that you just don't want to know.
2. For me and my wife to live a long, happy life together.
3. To have my all of my descendants live physically, mentally, and spiritually rewarding lives.