According to the producers, he actually recorded all his lines himself (as opposed to them just using the same voice software and getting an identical result) so evidently he must've been fine with making fun of himself in that way.
--
They Saved Lisa's Brain (1999):
Stephen Hawking: "Your theory of a donut-shaped universe is intriguing, Homer. I may have to steal it."
--
Anthology of Interest I (2000):
Nichelle Nichols: "It's about that rip in space-time that you saw."
Stephen Hawking: "I call it a Hawking Hole."
Fry: "No fair! I saw it first!"
Hawking: "Who is The Journal of Quantum Physics going to believe?"
--
Fry: "...so then my chair tilted back and I almost fell into this freezer thingy."
Stephen Hawking: "I call it a Hawking Chamber."
--
Nichelle Nichols: "Wait. I'm getting an idea. What if Fry was supposed to get frozen?"
Stephen Hawking: "Yes. Shove him in the tube. It was my idea."
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