Don't tell them they're beautiful!! I highly recommend making no direct reference to their looks. Women learn early to expect guys to like them only for their looks, and I'd be willing to bet most women consider that very shallow behavior. In a later message, you might mention that you like they way they look, but not until you've exchanged a few messages first.
Comment favorably on their profile in general, maybe say that you noticed you had a lot of things in common. Then comment on one or two specific things in their profile that you really did like. For example, s/he said she likes (pardon the cliche) pina coladas and walks in the rain, and you do, too, maybe you can tell a cute/funny story about one or both, or simply claim that those are your favorite things, too. Maybe expand a bit, ask if s/he prefers pina coladas with the big slice of pineapple or lots of maraschino cherries. Or if s/he prefers warm rain/cool rain/rain with wind...etc.
The point is to let them know that you actually READ the profile and didn't just look at the pictures. And, not only did you read it, you have the ability to comprehend what they wrote, and you can carry on some type of conversation about it.
And a little bit of humor, if you think the situation warrants and you are up to it, is always a good idea. Gentle humor, maybe a little subtle (but not too subtle), to see if you're on the same wavelength there. An example of that might be the time you went for a walk in the rain and it turned into a hurricane. Something that really happened to you that you can be genuine about. I think women may have radar for "genuine" - I honestly don't know if men do or not (I suspect not). Not that I haven't been fooled by non-genuine guys into thinking they're genuine, but women (even Aspie women) are a bit more attuned to that aspect than I think most men are.