Disable Flash in Safari for all but YouTube
You should give "Click to Flash" a try. I believe that it does pretty much everything you are asking for.

This plugin disables flash in Safari by default, but to load some flash content all you have to do is click on the "Flash" button in a video and the video will load and play as usual. You can even whitelist sites in "Click to Flash" so you won't have to click on flash videos when browsing YouTube.

I have not been installing Flash at all on any of my machines. I use Chrome for YouTube, since it has a sandboxed version of Flash.

EDIT: Almost as soon as I hit Post on my answer I noticed that "Click to Flash has been superseded by "Click to Plugin" which appears to do much more. I haven't tried this, but it looks like the only choice for Safari 5.1 and later.