The Electronic Frontier Foundation (EFF) has published a free software tool to check your connection for ISP’s bad behavior. It will spot IP packets which are forged or modified between clients, inform you, and give you copies of the modified packets.
Unfortunately for the non geeky users, there is no installer packages to easily install it on any Linux distribution, nor there is any GUI. Its a command line tool that you have to compile yourself. The project is hosted on sourceforge.net for you to grab if you’d like to make a package for it.
But anyway, its a great thing to have, if your ISP is messing with your traffic, you should know about it (and change ISP). I’ll be giving it a try soon, because I’m getting suspicious about this cable company in Monterrey city.
To run the tests, I recommend you to first use the wiki page. There’s a little guide to test different protocols.