I want to play a little joke on my friend. Is there a simple voice filter program I can use that has a Steven Hawking preset?
A shareware program named WillowTALK has a voice that’s pretty close. It’s apparently what Ken Leavitt-Lawrence used to create the MC Hawking recordings. It’s available at download sites like this one.
Macintosh computers have several voices to choose from.
It does help to be a freaking genius though… If you really want to pull it off.
That’s entropy or E-N-T-R-O to the P to the Y,
the reason why the sun will one day all burn out and die.
Order from disorder is a scientific rarity,
allow me to explain it with a little bit more clarity.
Sorry, I just love that stuff so much I couldn’t help but pimp it before the masses.
Using Macintosh voices will make you Fitter & Happier.
To sound more convincing, it wouldn’t hurt to get his name right: Stephen. 
If you want to sound just like Mr. Hawking, you’ll need one of these.
But it sounds like what you’re looking for is something you can speak into and have your voice sound like his. AFAIK, there’s no way to do this. His “voice” is entirely synthetic.
Many modern speech synthesizers use tiny snippets of recorded human speech and string them together. The DECTalk system that Hawking uses builds the entire signal from scratch.