Hazel eyes change naturally with light or mood; certain shades of brown hair (the kind that has blonde and red hairs mixed in and is often, unfairly, called "mousy") likewise change colour in different light or climate. I'm not sure this chameleon-like effect is specific to vampires.
I've also noticed a certain sharpness and clarity in the eyes, and I often search that trait out amongst my friends.
Sharpness and clarity come from an active mind and a direct, forthright gaze; since vampire-identified people are likely to be individualists and are also likely to have a certain mindset (if not actually agressive, at least alert) then that would account for the look in the eyes. Our society finds that sort of clarity threatening because only rare people possess superior intelligence and are actually encouraged to nurture it rather than stifle it, and of those free-thinking intelligent types, many do their best to hide that self sufficient streak in order to avoid appearing "rude." While I don't think that clarity and intensity of gaze is unique to vampires, I do agree that vampires are probably more likely to have it. most of us are outsiders of one sort or another.
Also, sometimes the features of the face are extremely unusual--as if, from another time.
How so? Small chins, brow ridges (as in homo sapiens neanderthalensis or homo erectus)? The reason I mention this is that facial features have not changed all that much in the past few thousand years. What has fluctuated is fashion; and things like eyebrow shape, forehead shape, hairline shape, etc have all been cosmetically manipulated at one time or another. If someone looks unusual, it might be due to something cosmetic: tweezing the eyebrows so heavily that they are almost invisible, for instance (which is what Europeans did in the fourteenth century) Or it might be due to odd bone structure.
I personally am the result of all sorts of minor cosmetic alteration. I dye my hair red; I use facial moisturizer that has a lightener in it, to keep my face white and translucent; when I have the money I plan to get caps on my teeth to straighten them and whiten them and even them out, having never worn braces as an adolescent. Eventually I'd like to get a boob job and replace my 32A cup breasts with 36D knockers. I wear clothing that not only feels natural to me, but which enhances my image. When I get contact lenses, I'll probably get a pair of amber-coloured ones to bring out the yellow flecks in my eyes, since my eyes only look pure yellow on rare occaisions.
It's all vanity, but it does indeed make me look...distinct. On the other hand, I freely admit that I spend a lot of time and money maintaining an appearance rather than just waking up, brushing my hair, and going about completely natural. I do my best to enhance or alter what Mother Nature handed me.
I am sure I am not the only vampire who succumbs to such vanity. In our society, physical beauty is considered almost next to godliness; if ordinary people can be insecure and vain, why not vampires?
I don't mean to refute your hypothesis/observation that vampires tend to look different. I mearely seek to offer a partial alternative explanation to the obvious "we're all alien and we look this way naturally, because we're so different." I've never considered myself inhuman, I just see myself as differently human.