Totally different. But depends on context. "would you like to come on Sunday?" Does not specify where. could be to a movie, on a trip, to the moon. "Would you like to come over on Sunday?" "come over" means "visit me", come to my house. . So they could mean that same thing, or not, depending on what has been said before ... would you like to come... . We're having a party here on Saturday. Would you like to come? . We're having a party here on Saturday. Would you like to come over. . Almost the same with context. I'm going to Spain soon. Would you like to come? (to Spain?) I'm going to Spain soon. Would you like to come over to say goodbye? (my house, now) I'm going to Spain soon. Would you like to come over to visit while I am there? (over the sea?)

There is no difference. It means the same thing.