This is a very tricky trend, I know a lot of people hate the ankle boot revival because they feel that it's yet another unfortunate throwback to 80s fashion, it only works for 6-foot-tall supermodels, it makes legs look chopped-up and all that jazz. However, fashion is about taking risks. And just like boyfriend sweaters, ankle boots are very hot if you know how to wear them right. That said, I believe that experimenting should not come at the cost of aesthetics, so Use Your Judgement. And the more experimental looks in this case should probably be reserved for those of you blessed with legs up to there.
The hardest look to pull off is bare legs and ankle boots. It can, however, work if the boots don't cover your ankle fully and if the colour matches your dress.
A safer route is to wear opaque (or sheer but dark) tights. If you have extremely long legs, you can experiment a little bit with the colour of the tights. If not, go for a colour that matches the colour of the boots so that the line of your leg will remain unbroken.
Even if you do have long legs, the best thing is to stick to dark colours or colours in the same family as the colour of the boots. Too much variation can be just as bad as bare legs. An elongating monochrome look would be very stylish. For instance, I just ordered this black wool skirt (on sale for $29.99!) from Gap, which I'll be wearing with black tights and black ankle boots. I'll probably add a dash of colour on top, but I'm going to stick to dark tones.
Or try longish leggings with just a hint of skin showing above the boot. I know public opinion is that leggings are so not cool anymore, but I think this is one case in which wearing leggings wouldn't have the fashion police chasing after you with sirens blaring. Especially with a long sweaterdress or a gorgeous tunic, this would be very chic indeed.
Trousers arguably don't let you show off your stylish boots to their fullest advantage, but trousers are much easier to work with. Almost any kind of trousers will be fine, and long after ankle boots have gone out of style, you can wear them with trousers and no one will be any the wiser that you're wearing something so (gasp!) untrendy.
Skinny jeans can be great with ankle boots as Kate and Sienna have demonstrated to the world, but like I've said a thousand times - most girls, unfortunately, are not Kate and Sienna. Which means, if you're uncomfortable with skinny jeans, don't make yourself a slave to fashion.
If you are going the skinny jean route, look at this picture of Mary-Kate, it's hilarious because that's an awful shirt, clearly it was the hairstylist's day off, and those boots bear startling resemblance to medieval torture devices (I think they're Balenciaga, am I right?) but ironically it illustrates a good way to wear ankle boots, even for petite girls like the Olsen twins.
Just do it with a bit more flair - lose the plaid shirt, go for something equally striking but more feminine, flowing, sexy. And don't make it a very high maintenance look. Don't just walk out with MK's bedhead but keep things simple. With your skinny jeans showing off those great boots, keep the other accessories to a minimum.
Or wear your ankle boots with a pair of cute pinstriped trousers. This look would work for internships, interviews, etc, and you'd feel confident and stylish without showing your (future) employers too much attitude.
Try ankle boots with straight-leg jeans or slightly flared jeans. Just don't wear them with widelegged trousers, because that's going to make you look like you have ambitions of working in the circus.
If you're feeling courageous, you could try ankle boots with cropped pants. Top it off with a killer jacket and it could work -- give it a shot if you're feeling experimental, but I would say this would be best if you had really long, lean legs.
Add a healthy dose of confidence and ready, set, GO!
(By the way, a trick for making your legs look longer-than-long in a hot minidress: wear nude shoes. Even Cameron Diaz with her Hollywood legs works this look.)