To my knowledge Gary Bash supports pretty much all Wrye Bash tags, so I would suppose it also supports import of eyes. As I'm only using one race mod (throttlekittys eyelashes) and Slof's Eye Retex, I haven't tried out the functionality.
Do you just want the eyes for your own character? I use Anthony Lings Coiffure and made my own plugin adding most of the other eyes available at Nexus to it. I have more eyes than I could ever use now.
Rivens Eyescapes has some beautiful and unique eyes.
SydneyB wrote a great tutorial in the description for http://www.fallout3nexus.com/downloads/file.php?id=6982. Just substitute Eyes wherever you see the word Hair and you'll be done in no time. I'd offer to send you a copy of my own esp but I've smooshed hairs, my race and even people into it at this point.
I believe FACE offers much more in the way of eye options.
Thank you! FACE was it. I am an idiot - this is what I was using, not that long ago really, but I got so heavily into Oblivion, leaving Fallout behind for a while, that I forgot about a number of (to me) crucial mods. :blush:
And thanks to all other respondents, as well. I'll look into the alternatives (and that tutorial) - who knows, I might be able to create the perfect mix, some time.