There are several different kinds of boots, and they fall under a number of different categories, but today we'll split them into casual and dress. Pretty self explanatory, but casual can be worn with most things while dress are best kept with suits. Ben Ferrari has some great examples of casual options in this slideshow for GQ.
Dress boots are a little more daring, so we'll go there first. Dress boots are typically leather and much more simple than casual boots. Boots with embellishments like buckles, plain boots and chelsea boots are the best to wear with suits. Some dress boots look sort of like a taller version of a dress shoes, and those work too. You want something that easily and invisibly fits under the pant leg and doesn't have too heavy of a sole for a formal look. They're easy to find at any store that sells men's shoes, but I advise trying them on with the pants you'll wear them with before committing, because it definitely gives the suit a different look.
Now for casual boots. There's a much bigger variety here, whether it's in color, sole type, closure type, height and style. Much of the choice comes down to opinion, but there are "norms" for wearing boots and what you should wear them with. Casual boots can go with pretty much anything you'd wear your casual shoes/loafers/boat shoes with. Jeans, cords, khakis, and the different colors those come in. Boots can really elevate the look of an outfit, but make sure your pants either fit over them, you will cuff them right or that you'll master the sloppy pant tuck. Desert, hiking, duck, chukka--there are lots of options, but for cooler weather and the possibility of snow in the not so far future, leather is good for the seasons to come, and the risk is definitely worth it. Take the chance, and make the investment.