I don't know actually. This is a question post so don't freak out if i don't give you an answer to my riddle. I'm sure you can make up your own. Anyways.... I have download a few mods and Now I am missing eyes on ALL NPC's and my Char. I'm not sure what it could be.
Here's my mod list;
VOILA
Male Body Replacer
(All)CM Partners
cm Kitty Cole
Cute elf(Although, i never activate or play, this is the only char. that actually has eyes.)
Oblivion Reborn
Beautiful People
Akatosh Mount By Saiden Storm

I really hope it's something minor.
Thanks for the help!

Supernatural.

Clearly a problem with Beautiful People. Why don't you try deactivating it? I'm hoping you're using OBMM or Wrye BAIN.

Unless you completely uninstall BP.......... Well, I wonder if the topic starter uses Male Body Replacer-Beautiful People compatibility plugin. I never recommend it, because that was for older BP, which retains eye mesh paths from Elaborate Eyes. BP 2.7 replaces default eye meshes with EE meshes. If you're using BP and Robert's male body replacer, I rather recommend to build a bashed patch with Wrye Bash(do not forget to merge Male Body replacer plugin, not compatibility plugin when building).