If you prefer HTML5 video to Flash, here is a method suggested by John Gruber to employ User Agent masquerading in Safari 5 to try to force sites to serve it to you.
If you turn on the Develop menu in Safari (Preferences » Advanced » check the box), you get the option to choose the User Agent string Safari will hand to a site to tell what browser it is.
From the Develop menu, Choose User Agent » Mobile Safari 3.2.2 - iPad and the site will switch to HTML5 if it supports it. You will need to refresh the page if you've already loaded it.
The setting will only last for the current browsing session. It can be made persistent using the following command (note that this is slightly different than the command linked to in the article; that one produced errors when I tried it in Terminal):
defaults write com.apple.Safari CustomUserAgent "'Mozilla/5.0 (iPad; U; CPU OS 3_2 like Mac OS X; en-us) AppleWebKit/531.21.10 (KHTML, like Gecko) Version/4.0.4 Mobile/7B334b Safari/531.21.10'"
defaults delete com.apple.safari CustomUserAgent
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