Based on this image, this is a list of my favorite waifus from each season and special categories, going by the following rules:
1. A character from the Mane Six cannot appear in any category other than the "Mane Six" category (otherwise Pinkie would also be in the Season 1 spot).
2. Each of the Seasons, Equestria Girls, and Movie/Specials categories can only include a character whose first speaking role was in that category (Marble may have first appeared in season 1, but she didn't speak until season 5 — I'm counting her "mmhmm" lines as speaking).
Lightning Dust and Autumn Blaze are pretty much there by default — there weren't many characters to choose from in those seasons.
A close runner-up for season 7 on my list is Meadowbrook. For season 9, Shimmy Shake is a close runner-up.
Sonata Dusk is a close runner-up for Equestria Girls (though if I didn't have rule 1, I would have had human Pinkie as the character for Equestria Girls, since she's technically a different character than pony Pinkie).
And sure, Petunia Petals may have gotten engaged to Sunny Skies, but her personality was the one I found most attractive of all characters introduced in that special (and the movie), so I went with her (and Pinkie ends up with Cheese Sandwich, so clearly I'm not factoring in relationship status to this).
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