It's surprising how many websites still require Flash to view video when using a desktop browser. I use the technique described in this Daring Fireball post to change the user agent string in Safari on OS X, making it look like Mobile Safari in order to get HTML5 video. This does the trick about 90% of the time. I find that the YouTube 5 Safari Extension also helps, often making the user agent shenanigans unnecessary.
I used to keep Google Chrome installed as a fallback since it comes with Flash preinstalled. I find I need to use that less and less, though.
I use two Keyboard Maestro macros for this. The
Toggle iPad UA macro
(bound to ⌘.) toggles between the Mobile Safari for iPad user
agent string and the default Safari user agent string. The
Open in Google
Chrome macro (bound to ⌘⇧.) opens Safari's
frontmost tab in Google Chrome.
Both macros are available on Github.