well keep in mind yaoi is yaoi, you're probably not gonna find something completely unique to the genre that's a comedy, but I'll try to pick the less cliched ones...and also keep in mind what's funny to others may not be funny to you. Here we go
http://www.mangago.zone/read-manga/datte_maou_sama_wa_kare_ga_kirai/ it's kinda different, I thought it was quite funny...the seme is mildly evil and there's some dry humor in it...if its not your cup of tea then that's ok....
http://www.mangago.zone/read-manga/kirepapa/ the uke is pretty funny actually. In fact there's some side stories about his family and they are all relativiely funny. Short uke with a pretty impressive temper, but he's not all that bright.
http://www.mangago.zone/read-manga/nar_kiss/ shounen ai but I think towards the end there's sexy scenes. The uke is ridiculous...if you read the synopsis you'll understand I think
http://www.mangago.zone/read-manga/yume_musubi_koi_musubi/ uke is pretty entertaining, and I found it to be a sweet read just anyways...
http://www.mangago.zone/read-manga/kono_ore_ga_omae_nanka_suki_na_wakenai/ gigantic misunderstanding and a narcissistic uke...pretty funny.
http://www.mangago.zone/read-manga/hatsuai/ unique and odd but pretty funny
http://www.mangago.zone/read-manga/sono_koi_ni_wa_wake_ga_aru/ its cute and I didn't think as cliche'd....but less laugh out loud funny it's more one that makes you grin and go aaaaaw.
http://www.mangago.zone/read-manga/10_dance/ there are some laugh out loud moments but I thought it was also well developed as far as their relationship and the tension.
http://www.mangago.zone/read-manga/19_days/ shounen ai full color super well done and he tian is absurdly runny, and kinda realistically a teenage boy.
http://www.mangago.zone/read-manga/scandalous_seiryo_university/ seme is bizarre and sadistic in a very silly way....it may not be your cup of tea but he's sorta sweet with the uke he's just kinda evil to everyone who's not him.
http://www.mangago.zone/read-manga/dekichatta_danshi/ there's some laugh out loud moments and some heart jerking moments and warm moments its sweet, but keep in mind its a yaoi manga.
Hopefuly you like some of these they were the ones I thought I could find that came the closest to your request.
Kizudarake no Airabuyuu!
*and Gakuran Ninpouchou
http://www.mangago.zone/read-manga/adekan/ Unfortunately it's Shounen ai, but it's funny and has an interesting plot.
http://www.mangago.zone/read-manga/neko_samurai/ Parodies the cliches found in yaoi
http://www.mangago.zone/read-manga/datte_maou_sama_wa_kare_ga_kirai/
And there was one about a romance between a guy and his PC (personified), but I don't remember the title ( ̄へ ̄)
Laughing out loud was my criteria for this list, but humor is less universal than you'd think. http://www.mangago.zone/home/mangalist/13870/
http://www.mangago.zone/read-manga/ai_to_yokubou_wa_gakuen_de/ This one has some hilarious couples...its a bit smutty and there's a lot of different couples but there's some I really like. Its super long so its good if you're bored and want some light entertainment
I feel like I've read all the really funny yaoi with interesting plots. Any recommendations? I bookmarked some from lists but so far haven't come across one that actually makes me laugh out loud. Most have a couple funny scenes but overall stick to cliché plot devices like falling for the rapist etc. Help!