Great recommendation, but I'd say the torch has been passed to the bona fide Safari extension of the same name:

http://www.math.northwestern.edu/~hoyois/safariextensions/cl...

One benefit that the original ClickToFlash has compared to the extension is that it works with web content embedded in applications other than Safari.

Just disable all plug-ins & Java in Safari preferences. It's a lot easier and you won't miss them. The only thing I used Flash for was watching videos, and HTML5 has that mostly covered now.