As an avid Mystery Science Theater 3000 fan (I own nearly 30 of the boxed sets of DVDs), Werewolf is one of my favorites. I saw some references in online material to the episode being a bit edited—which was fairly common for MST3K—and I noticed that I could get the original on DVD inexpensively so I decided to go for it and see what the differences were. Of special concern to me was whether any of the jokes depended on the edits, because that would seem a bit like cheating.
First, I’m happy to report that none of the jokes were cheated. Well, that’s not quite true; there was one joke which had a little bit of context which was edited out, though of course one never knows whether it was the MST3K editors who removed it for the edited-for-TV editors who removed it. That joke was when Natalie tells Paul, “you may just be our last hope” and (IIRC) crow says, “maybe some day they’ll tell us what he’s their last hope for“. Earlier in the film there’s a scene in the original in which Natalie tells Paul that they’re running out of research funding and their efforts to secure more have failed, and Paul offers to use his writer’s talents to try to help them write better grant proposals in order to secure funding. Or maybe to use his connections. It’s not made explicit, as I recall. However, there is also a scene left in the MST3K version where Natalie tells Yuri that Paul is going to try to help them get more research funding, so the editing wasn’t exactly unfair to the movie here, though it certainly wasn’t helpful.
Some of the editing tightened the movie up and made it better; in the original there are some endless driving through the desert scenes a bit reminiscent of the credit-scene-without-the-credits in Manos: The Hands of Fate (though not as long as in Manos). Most of what was cut out were some sub-plots which did make the movie overall better though weren’t related anything Mike and the bots said. For example, there’s a sub-plot where the real estate agent is into Paul and he (gently) rejects her advances and so she tells him to walk home and leaves. This explains why Paul is at the party alone and in a position to meet Natalie. It also somewhat explains what the real estate agent is doing back at Paul’s house later to be brutalized by Paul-as-werewolf.
Overall, my impression was that while the original movie was more complete, it was also more sloppily edited; so, basically, something of a wash. I do recommend watching the original if you get a chance, if for no other reason that you see the raw materials that went into making such a good episode of MST3K. It’s not a high priority item, though, as it’s about 90%-95% the same movie, and certainly the main plot is 99%+ the same. It still doesn’t explain why Natalie became a werewolf at the end of the movie, though. (I’ve never understood why the crew makes fun of how obvious it is that she was a werewolf; the setup as we slowly pan in was a bit telegraphed, perhaps, but nothing in the movie really led up to her being a werewolf.)