Other answers seem to be looking at this from a legal standpoint, but it sounds like you are talking more conceptually.
First, note that Parody and Homage are two very different categories; in the former case you're ridiculing the game's weaknesses, in the latter celebrating its strengths.
I would say in either case, the question of when you cross the line to "just another ripoff clone" is answered by whether your game adds anything new to the discussion.
For a parody, your game should not just be copying another game's mechanics, but it should be engineered to point out the flaws in the original in a way that the original game does not. For example, a parody of an old-school CRPG might not only have the player do a meaningless treadmill-grind for XP, but constantly remind them of how meaningless this is and how the game is just artificially increasing their required play time. Or it might eliminate the grind entirely, shortening the entire epic 40-hour experience to five minutes. In either case, the original game's mechanics are selectively copied (or not) to showcase a weakness with the form. To tell whether you are successful, I suppose a worthwhile question would be, "after playing this parody do you feel different about playing the original game?"
For an homage, you should be taking the original game further, improving it in some meaningful way. Here the question would be, "what reason is there to play this homage game, rather than playing the original?" and you should have a good answer!