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I am agree on it that unusal videos and audio on a website or a background music that automatically starts, many a times annoy to the visitors. There should be a manaully controlled button on the website if having any video or audio. What to avoid while designing a website? read here http://blog.pixelcrayons.com/web/some-web-designing-mistakes-you-should-...
The whole auto-play ad thing would be more of a poor choice of who or what to use for advertising than a poor website design, but still very annoying. As for annoying website design I would say anything with flash or splash page before any actual content is displayed. The next annoying design are site that the sub-pages that don't fit the same theme as the front page or just overall theme. I use Firefox with NoScripts, along with AdBlock. NoScript takes some skill on what to allow or not, but definitely cuts ads and adds a bit more security.
Autoplaying video or audio are right up there with me too. Another one that I think is a mistake is click-through slideshows with no option to view all. I understand the desire to get more page views, but the result for me is that I'm likey to simply leave the site instead, therfore there are actually fewer page views. I would like to see some analytics with the same website trying both click-through and click-through with a “view all” option and see which was actually more effective, instead of relying on my personal likes and dislikes.