In no particular order:
Birkal
DougJustDoug
paintseagull
SoIheardyoulikeSENTRET
Yilx
I'm really surprised that Birkal isn't getting more votes (or maybe I just haven't noticed them). It's definitely the cutest of the submissions, it has a great and original concept behind it, and I think that it looks more like a believable Pokemon design than almost any of the other submissions.
I also think that paintseagull has a great concept that will unfortunately probably get overlooked by many; to be honest something about it doesn't quite look "finished" to me, but I still think that it deserves consideration for its clever and unique approach.
I must admit that I didn't like the entry from Yilx at first, but the beautiful supporting material really turned it around for me.
I don't think that I can say anything that hasn't already been said when it comes to praising the entry from DougJustDoug. The concept is great, the story is great, and the design is great. I just really wish that there were more visual supporting material behind it, and I was a little bit disappointed to see that the artist was so unwilling to change anything about the design after getting community feedback. All of the other top contenders really took to heart the feedback that they got, and their designs grew because of that. Fortunately, this design really was very strong to begin with.
Finally, I SoIheartyoulikeSENTRET definitely has my favorite entry. The artist took the cliche jack-o-lanterns and scarecrows that I was sure would absolutely plague the submissions and created something that's conceptually basic but still extremely endearing, which is exactly what some of the best official Pokemon designs do.
Edit: Just because I feel like commenting on why I didn't vote for what appears to be the most popular submission so far:
Mos-Quixote has a really cool concept, and when the Sketch concept was initially selected, I could easily have seen this entry winning. Unfortunately, it looks like the artist began designing it before the typing was selected and then chose not to change anything about it after the typing was selected. This is a fantastic design, but not a single thing about it feels "Grass" or "Ghost". Paper coming from plants is a huge stretch, and none of it feels creepy or ghostly at all. This feels like a Normal-type pokemon. If I saw this design, I would never in a million years guess that it was supposed to be Grass / Ghost, and I think that's a big problem.