Compliments are always great. I really like my eyes believe it or not, their one of those body bits I'm quite proud of, so I quite like it if a girl compliments them.
Its a real positive for me specifically, because it sort of implies that your looking into my eyes. I believe that you can see a lot of a person in their eyes, so to me, you complimenting my eyes would mean that you were complimenting me in general, on a more personal spiritual level.
It would depend entirely on how they were complimented to whether I thought the girl liked me or now.
If a complete stranger came up and told me she liked my eyes, I'd probably be a little weirded out, but I would like the compliment. Especially if I thought the girl was good-looking ;)
If someone I knew a little but not very well said it to me, I would probably be surprised but thank them for the compliment.
Also it would depend on the tone. If it just sounds like the girl is saying it because she wants to freak me out or mess with me a little, I wouldn't like that too much. It would seem like she's joking or something. If she says it and sounds sincere (and this is true for any compliment, really), I would be flattered.
Love that compliment, I think eyes are one of the most genuine features on a person, its hard for a person's eyes to mask things. I wouldn't necessarily suspect the girl likes me unless the compliment is coupled with something more.
There is a guy at my work that I never really noticed his eyes but when I was on his facebook page I noticed on a pic of his how nice his eyes are. I wanted to tell him "nice eyes" but feel that I can't tell him that so I keep it to myself.