Plenty of things can cause this, I've seen it too. Starting from the obvious:
There may be something in the Internet causing issues, like storm damages in the infrastructure or just your ISP. Not much you can do about these.
Then again it might be your router and/or its built-in firewall.
Or it can be your anti-virus checking each package, choking after every 30 packets or so. Putting the game in to the ignore list might help if you don't dare shutting the whole thing down during gameplay.
Other background programs may share the Internet connection for their own purposes. It can be anything from a printer program or Flash Player or Windows checking for updates up to a bot sending trash mail without your anti-virus knowing it. Disabling automatic updates and minimizing background processes will help.
Failing hardware can cause some issues, too, especially if you have overclocked your system up to its limits.
There may be other things, too, which I can't remember or don't know of, but hopefully this will serve as a starting point.
