It's just all about tenses. Please bear in mind that these are unreal sentences. In other words, they never happen. So, they are obviously positive but the meaning is negative and vice versa.
Remember that the second sentence is about some that does not happen in present tense:
I wish you came. (It means you do not come. Imagine you have a weekly party and your friend never shows up. In this case, you say, "I wish you came to our party.")
The third sentence signifies a situation in which something might or might not happen in the future. In other words these sentences show your wishes for future. Just imagine your neighbor is playing a music loudly. In this case you say, "I wish they would stop it." Also: I always have to get home early. I wish my parents would let me stay out.