Making your own animations and games: Flash vs. Javascript?

I'm coding my own graphic novel website, and am thinking about making some games or simple animations for it. The only problem is...

Flash: Supposedly Flash can actually hurt a website's ratings in search engines, and anyway it requires certain plugins

javascript: Many users disable Javascript in order to help avoid advertisements

Java: A big, scary programming language that I won't be learning any time soon

Any recommendations on which choice is the best?

Flash, as that it is one of the most widely used tools used by websites. Flash is also really good for making games, as it allows many objects to be played within a flash movie.
And for the plugins, these days most browsers already come preinstalled with the neccessary plugins to play flash.

Javascript, in my opinion, wouldn't be suitable for an entire site like that solely for animations.

As for Java, yes, and Java applets anyway can be slow.

Overall, flash seems like your best choice. I know that NBC has flash graphic novels about certain shows.

Good luck with your site!