First up is a big one: character designs. Now, after making my choices for this list, I've realized that I have only one main hero(ine) on the list. I believe this is because the main characters in Vanillaware games tend to have a more simply design (well, simple by Vanillaware standards), while antagonists or side characters tend to have more intricate designs. The reasons for this is because antagonists have to be imposing, and thus need more detailed or exaggerated character designs; furthermore, these detailed designs don't need to be animated as much as the main playable characters, thus they can have such detailed designs.
Also, it goes without saying that choosing a "Top 5" for anything involving Vanillaware is pretty hard, and most are almost certainly going to disagree with my lists, heh.
And with that said, let's begin with #5 ...
5) Chartreuse Grande