I'm coming from the perspective of a daughter who was and is pretty gender non-conforming, so my advice may not be useful generally, but I hope it helps anyway.

I think other commenters have talked about not saying "Girls do this" and "Girls don't do that", and an important aspect of that is to not be inherently dismissive of feminine/masculine attributes as whole. If she ends up being the only geek-ish type girl she knows, it becomes easy to dismiss the "feminine" interests of her peers as lesser compared to her own. So, expose her to media with significant female characters, but not just those who resemble her or share her interests. Actually, come to think of it, expose her to real women with varied interests, to avoid the whole categorising thing as much as possible.

Regarding clothes,which is an area in which I have frustrated both my parents very much, follow her lead where possible from young. If you have an occasion where a dress is required because of formality but she's clearly upset/angry at wearing a dress, see if there's an appropriate alternative. Whatever the outcome, don't make it feel like it's her fault for being uncomfortable in dresses. Also, children can change rather quickly, so remember that both the little girl who loves MLP and the little girl who loves Star Wars may not stay that way when they grow up.

I'd just like to add that I sincerely respect you for choosing to ask for this advice at all, since most parents never bother.