I've been getting into road racing more and I've noticed that there are lots of different sites for registration. For example, it seems like in the midwest, a lot of races use truesport, but back in the NY metro area, most races use bikereg. I guess my question is, what are the most popular sites that I should keep my eye on?
You're going to figure out what the best system for your area is. Any good local association should at least keep a centralized, regularly updated calendar on their website; unfortunately, some are not so good. Of the local associations I have experience with, TBRA (Tennessee) and GABRA (Georgia) are pretty damn good, NEBRA (New England) is okay, LAMBRA (LA/MS) is iffy, and ABRA (AL) is worse than useless. For example. In NEBRA, it's not a big deal that the local association website isn't great, because pretty much everything up here is on BikeReg, which can work as sort of an unofficial local calendar.
I was surprised to learn, when I moved to Tennessee, how regionalized race registration is; you wouldn't expect physical location to matter for online registration, but apparently it does. So, as I mentioned, here in New England, you register for almost everything on bikereg.com. Whereas, in Tennessee, there were a few different websites in use, but with the advent of USA Cycling's in-house online reg system, pretty much every race uses that - but before that happened, it still wasn't a big deal, because TBRA's website and race calendar are and were excellent and made it easy to find out what races were happening in the state. And so on. You're going to have to look and ask around and figure out what's best for the regions you're playing in.