I wouldn't consider myself a big manga reader, but judging by the bit I've read these are my top choices that I would like to see in anime form. I did not just go about and pick my favorite manga from my list, but tried to imagine which ones would translate into an anime better and to avoid ones that could easily go haywire.
So, in no particular order:
20th Century Boys + 21st Century Boys: Come on, now! This one seriously needs to be made. I haven't read the Monster manga yet, but judging by the Monster anime (which was amazing) I am sure 20th Century Boys is more epic. And who doesn't love epic?
Kimi wa Pet (Tramps Like Us): One of my favorite josei titles. I think this would translate very well into an anime; which is not often the case with this genre.
Yotsuba&!: I think this one has the most chance of being turning into an anime from the rest on this list, but I am a little scared that they'll ruin it. I loved the Azumanga Daioh manga by the same mangaka, but did not enjoy the anime adaptation. So, we'll see.
Hotel: This would make a very epic little OVA if they ever set out to do so.
Aisuru Hito: My favorite josei manga as of yet. A little reluctant putting this one on the list as well, because when something is so good you don't really want to mess with it. But if done correctly this would earn an easy 5 star rating from me anime-wise.
Venus ni Arazu: Same mangaka as Aisuru Hito (a mangaka I am quickly becoming a huge fan of). The humor reminds me a bit of that in Skip Beat and since that anime turned out well (despite me being desperate for another season or 10) I think this would do well too.
X-Day: Very engrossing manga that deals with issues you don't see too often explored to this depth. I would love to see this made into an anime.
After School Nightmare: Same mangaka as X-Day, ASN explores different themes, but ones that are no less difficult than covered in X-Day. I would really like to see more serious anime and this would definitely be a good one.
Gyo: Ah the famous "GASHUNK!" speaks for itself I would think. I think all who have read this manga look forward to a day where they can hear that line once and for all. UPDATE 10/12/11: THIS ONE IS BEING MADE INTO AN ANIME!
Uzumaki: I discovered that there is a Live Action version of this out, but I'm not going to watch it. I think the creep factor would be lost in it, but an anime would have a better chance of keeping true to the terror of the spiral without it spinning into ridiculousness.
Goth: Was a very graphic, disturbing, and creepy manga that I honestly wasn't that crazy about as I was reading it. I squirmed through the whole thing, BUT though I might be scared to watch the anime I think it would be a very good adaption. Some scenes that I remember would be 10x creepier were they accompanied by music/movement. Fans of Gantz and Narutaru would appreciate this one.
Saitama Chainsaw Shoujo: What started out as me reading a random manga alone- turned into an #ISSUP group read of sorts. That always makes it more fun, but when everyone started swearing that *I* was the main character (AKA scorned glasses chick with a chainsaw and a chip on her shoulder @.@) we started assigning roles to other ISSUP members. Plenty of good fun and if this were made into an anime we could do it all over again. Heck I'd be willing to do a fandub just for laughs.
Nekrateholic: This may just be the ladyboner talking, but I think anime really needs more gay vampires that like BDSM. Yeah... :D~
Mankai Darling: Super super cute yaoi manga. Not really explicit, but plenty of the "awww" factor that I just love in this type of story. I think a little OVA could do this story some justice in a genre that disappoints so often in anime. If it weren't for Junjou Romantica I might have lost hope by now.