Strictly according to the rules of grammar all three mean something different. The differences is in the tense. 1. "I wish (that) you had come" means: 1. something happened in the past 2. you were not there 3. I wish that you HAD been there! To use your example: yesterday there was a party, which I attended. You did not come. So I might telephone you to say that 'I wish that you had come!' 2. "I wish you would come" is the equivalent in the future. Eg. there is a party next week. You are saying that you are busy and will not come. So I telephone you to say: 'I wish that you would come!' 3. "I wish you came" strictly according to the rules of grammar is a habitual present. For example: I go to a chess club EVERY WEEK. You have never come. I telephone you to say: 'I wish that you came!'. BUT! the reason for which this is so confusing is that most people do not use these tenses this strictly, so you have probably seen all sorts of examples that do not match what I am saying. For example in the last example (3) the person telephoning their friend might also say 'I wish that you would come!' People also often say 'I wish that you were coming'. You might say this to your friend as you are about to leave the house, and try one last time to get her to come with you, but you really know that she will not come. If you think that she might still be convinced to come, you would rather say 'I wish that you would come!' Example 1 has the strictest sense and cannot be exchanged with another: 'had' makes it clear that it refers to the past. I hope that that helps.

Dear Aude, 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.