I recently read Koketsu Dining and Mauri to Ryuu and have fallen in love with the twisted idea of an uke having sex/relationship/whatevs with an actual animal seme. I know it sounds twisted, but I don't think we're here to judge, hehe c:
werewolves don't exactly count, unless he's doing it with the seme while in wolf shape.
just.. yep. that's the idea of it. I wish to see an uke together with a seme that is a beast/monster/animal.

and please, NOT a seme that just has cat ears or something like that, that's not what I mean :c

http://www.smackjeeves.com/comicprofile.php?id=135230
yaoi webcomic ._.

Mauri to Ryuu and Koketsu Dining are SO CUTE! Ugh, I love them so much. ahem

This seems to be a tough genre to find. Anthro/Intelligent Beasts seem rather uncommon, and if you're not careful you can come across some really gross stuff :/ I have seen some beastman/human stuff here and there in Bara genre (if you like that art style) though. Here are some general yaoi/shounen-ai that might come close to what you're looking for though.

Momo (KUJU Siam) features a guy who can turn in to a lion, and he and his lover do things while both in human and lion form. Not sure what the plot is though :/

Equus. Centaurs, nuff said.

Hide and Seek chapter 9 and Teirui Makura chapter 5. Werewolves who look pretty human, but they are more wolfy than most other werewolves I've come across, and they references more, uh, non-human anatomy once or twice.

I've always liked human-nonhuman romances (vampires, werewolves, demons, robots, aliens, whatever!) so I'll be watching this topic.

Wild Wind has a very short scene towards the end when the seme in the beast form is giving the uke a blow job.

http://myreadingmanga.info/3745house-spoil-dog-gintama-dj-cn/
And this Gintama dj is....a unique one. Ha ha. I'm not sure if it's your cup of tea. And it's not translated either, but the sex scenes are...I'll leave it to you to comment on.

Junketsu Ningyo - collection of animal transformation stories. It's been a while since I read this, so I can't remember if it's the seme who is the 'beast', or if he stays in that form while 'doing it'. But it's an unusual collection.

Inu mo Arukeba Fallin' Love maybe, again, I don't remember if he stays 'that way'

Renai Chuudoku - insects

Try these categories: Animal Transformation; Anthropomorphism; Human-Nonhuman Relationship

Bump~

Would love to hear more recommendations.

You should try

Kemono / jingai Bl
http://www.mangago.me/read-manga/kemono_jingai_bl/
Collection of short stories of animals and human relationships! It's a winner!!!!!
Especially chapters 1 & 4!!!!