[lvh]

When I was in high school, the teacher often used:

http://www.walter-fendt.de/ph14e/

Which are Java applets. Not quite as good as modern JS would be, but given the era they were written, they were pretty cool things.

[edtechdev]

There are a ton of excellent physics simulations here, too: http://phet.colorado.edu

Although they are also not done in javascript, but a mix of java and flash.

[dbaupp]

As a student, I enjoyed playing around with these: http://www.falstad.com/mathphysics.html

(All are Java applets.)