Websites with viruses or trojans should be set aside and not discussed, because they are not even worthy of being talked about in terms of "user experience."
1. Changing the browser's homepage
This is one of the most common rogue behaviors. Some websites directly change your homepage without telling you, some ask if you want to set their page as your homepage when you enter it, while others prompt you to do so when you're leaving. The purpose behind this is often to increase page views (PV), as if they're afraid no one knows about their website. Don't they know users hate this? After many people have their browser homepages changed by these websites, they don't bother to change it back—either because they don't want to or they're too lazy. They simply don't care what the homepage is. Rogue websites just love this.
The best example of this was hao123.com's homepage modification in its earlier days.
2. Pop-up ad windows
Especially with portal sites and certain email services, a small advertisement window will pop up as soon as you open the homepage, followed by another full-screen ad. For the sake of profit, can they really be so unethical?