Well, if said end user had a rooted Galaxy S3, they could use Darshak on their phone to check for "baseband attacks" that indicate they are communicating with a rogue tower. There's a company called ESD that sells a "cryptophone" that can do the same thing, but for a hefty price tag (like 1,300 USD!). Edit: Here's another cool app I found from a comment by @wesleyac: Android IMSI Catcher Detector.
Unfortunately, no one seems to have a good explanation of how it's done. But ESD does release the source code for their phones freely for security audits, and the SecUpwn group has released their app on Github. If you want to wade into the implementation details, that would be a good place to start. A brief technical explanation of the GitHub app is here.
These towers seem to be the modern-day number stations. We may never know, but we'll always get that creepy feeling when we think of them ;)
(I am not affiliated with either of these products.)