Where should I be rubbing my Pokémon?

Solution 1:

If you play with sound on, the rubbing noise (the 'wipwipwip' sound) changes in pitch as you find 'sweet spots' or 'bad spots'. The higher the pitch, the more the Pokemon enjoys it.

Short of facial expressions/body language, this has been the easiest way to figure out the sweet spots for me.

There is a thread over on GameFAQs where people have been sharing good/bad areas to rub as well, if you still cannot find a good place to rub, it may be listed there.

Solution 2:

From my experience, there is no one guaranteed place that's good for rubbing (either Pokemon or otherwise...) There is one thing you can do to make sure raising your Pokemon's affection though.

When you touch your stylus to the screen to rub your Pokemon, watch their expressions before you actually rub. Whenever their eyes form an upside-down U, that's a good spot to rub. Watch out if they make a pained or annoyed expression though, that's generally not a good spot.

For Pokemon lacking a way to express facial expressions, pay attention to body language. For example, if Butterfree tilts its head back/up it generally means that the Pokemon is enjoying the rub. If it seems to not move at all, it's generally a bad spot.