ACD Labs: Chemsketch – free modelling software
It’s not really a video, but you can build molecular models and make them move around on the screen, so it just about qualifies. It takes a wee while to get used to, but is worth the effort.
Demo videos here. Manuals here.
DP Bio teachers can use it to satisfy the modeling software stipulation of the 4/PSOW form. Enjoy!
EDIT – there is a shareware ($24.95) gif to flv encoder available here. I haven’t found any free software that can convert gif animations to flv files, so if anyone can help out, please let us know.
I have put a simple Chemsketch tutorial on making and animating glycine (word 2007 doc and SMART Board notebook file) in the downloads box on the right of this blog.
EDIT AGAIN:
The joys of Chemsketch are almost limitless. Here is proof: 
Posted on November 23, 2007, in Chemistry, Chemistry of Life (Core & AHL), Free Resources, Simulations, Software. Bookmark the permalink. 2 Comments.
i-Biology 
Where do I find the word document for the Chemsketch tutorial on making and animating glycine? I can’t find it anywhere?
I’m sorry – this is a very old post. Since then I’ve moved schools, countries and computing platforms. If I do find the sheet, I’ll post it here, but glycine is the simplest possible amino acid.