Bad design alone doesn't make a website malicious, but here are some cues that you might want to navigate away. If you're bombarded with flashing ads and pop-ups, and the focus of the site is to advertise and not to provide content, beware!
Pop-up ads on a Web site are annoying, but chances are they're not hurting your computer, unless the site serves up so many that your computer slows down dealing with all of those new browser windows. The sort of pop-up that should send up a red flag, though, is any dialog box that appears when you first pull up the site, before you've tried to actively download anything. If you load a download site and a dialog box -- a pop up box with a message or warning and the option to click either "OK" or "cancel" -- appears, do not click OK! You could be giving permission to install something – which could be malware. Instead, close the website immediately [source: Malware Prevention].
There are some pop-up ads that masquerade as these dialog boxes, and these external ads don't necessarily mean the download site is malicious. These ads look like mini browser windows and may appear without the address bar at the top. A real dialog box will just contain the message and the OK and Cancel buttons.