Geordie LaForge?
I mean, he traveled back in time to help Zephram Cochrane build the Warp Drive, AND he had the BCV on. That’s pretty nerdy.
Dunno about nebbishness. He did seem to have problems with getting women to notice he was there.
I forgot the best-known macho, tough guy Jewish protagonist in American pop culture… but he’s a TV character, not a movie character:
Detective Lenny Briscoe, played by Jerry Orbach on “Law and Order.”
Oh, and does anyone remember this one:
http://www.us.imdb.com/title/tt0072228/
Two Jewish cops known as Batman and Robin (based on a true story, and directed by Gordon “Shaft” Parks).
His father was Jewsh. He was raised Catholic, though the implication was he’d married and divorced one, possibly two, Jewish women, and through one had a daughter who was eventually murdered.
He might not qualify as Jewish in the eyes of an Orthodox rabbi, but I still say he counts.
There have been movies and a TV series based on Ed McBain’s 87th Precient detectives, including one named Meyer Meyer who is definitely Jewish.
Also, James Gandolfini played a gay mobster in The Mexican.
Rumour has it that the Coen Brothers have signed on to make a film based on Yiddish Policemen’s Union.
Likelyhood of a nebbish dork protagonist? Nil. Likelyhood of badass take-charge Jewish heroes? Tons.
I’m looking forward to it. 
Do TV miniseries count? Cause I have vague memories of somewhere in the depths of time seeing a miniseries with at least a large part about the Warsaw ghetto uprising and another about Masada. Sure, the jewish characters lost both times, but they weren’t whimpy losers by any definition.
This is also why I liked the short-lived Goodman series Normal, Ohio. Nothing like John Goodman and Dan Ackroyd in a man-smooch to bust stereotypes…
That was probably Holocaust.
Speaking of TV, the HBO series Rome featured a Jewish thug/enforcer.
And as for gay tough guys, how about The Dane from Miller’s Crossing?
If you expand your search into books, read this one page for an example of a truly tough kick-ass gay character:
You just can’t get much tougher than that! 
I wish more movies had peculiar subplots that went nowhere. As long as something doesn’t appear to actually be the main plot I don’t mind too much if some things aren’t resolved. Coen Bro’s movies are an exampe: I could actually see them, for one, having a movie with a relatively tough-guy protagonist who happens to be Jewish without it being either a joke or a plot device.
Heh, this reminds me of one of the more annoying literary “rules” I’ve come across: Chekov’s Rifle. Basically, the idea is, if Chekov walks into the room in a scene and hangs his rifle on the wall, then the rifle has to serve some purpose in the story or else it has no reason to be there.
One of my goals in life is to right a story where a guy named Chekov walks in, hangs his gun on the wall, and does absolutely nothing with it for the rest of the story. Maybe even grabbing a different gun if he needs a firearm later on.
Classic example, the Simpsons episode “Pokey Mom”. Marge has taken an interest in an artistic convict (voiced by Micheal Keaton) and, upon his release, gives him temporary lodging in the basement:
Marge: I hope this is okay. It’s not very prison-y.
Jack: It’s more than I deserve, ma’am. Now, which way is Mecca, 'cause I got to do a little praying.
Marge: [uncomfortably] Uh, Mecca? Well, let–
Jack: [laughs] No, I’m just yanking your chain. I’m Jewish!
For some reason, this cracked me up and it’s of absolutely no significance to the rest of the episode.
It’s a romantic comedy, not an action film, but in Keeping the Faith Ben Stiller plays and almost totally non-stereotypical Jew, and a rabbi at that. (Ed Norton plays a slightly more stereotyped Catholic priest.)
Both men, while not exactly badasses, play strong, athletic, non-nebbishy characters, and Stiller’s is rather hip and iconoclastic, trying to liven up his sermons and widen his congregation.
He is also sexy and virile and gets Jenna Elfman, who is sexy enough to tempt Norton’s character to break his vow of chastity.
So maybe not exactly what the OP was looking for, but a strong, positive Jewish character. And a funny, enjoyable movie, too.
It is very rare that the religious beliefs of a character come into play. Now I don’t know if you mean Jewish by birth or Jewish by faith. Is Batman a Christian? Is Hancock a Baptist? Is Wall-E a Hindu? Indy Jones did get married in a church, some sort of Protestant one, (IIRC) but his faith is not really part of the movie.
I think I’ve said this about three times already but: Judaism is more than a religion, it’s a culture, an ethnic group, and the stereotypes about it are not religious stereotypes but ethnic ones. They rely on things like the looks of the character, his last name, and the actor who plays him, much more so than anything stated about his faith. The faith has nothing to do with it at all. It’s all about cultural stereotypes.
There are some fairly baddass Jewish characters in Guy Ritchie’s film “Snatch”. Also there is a Jewish mob leader in the film “Lucky Number Slevin”.
Woody Allen “laudable?” To whom, by whom, and since when? He’s very funny, but his characters are miserable human beings and everybody knows it. That’s been his schtick since he got started.
You’ve got this whole thing backward: the stereotype of the weak Mama’s boy Jew is much older than Woody Allen (who at most helped create or update a stereotype of the New York Jew- which is now dated). If Allen is lauded, it’s for being an exceptionally successful filmmaker and perhaps for depicting characters his audience recognizes. As far as “giving his people a bad name” goes, people who think all Jews are snivelling wimps don’t watch Woody Allen movies.
I think your broader point has some merit - and pointing out that Bruce Willis had one Jewish parent or that some period dramas include historical Jewish mobsters doesn’t really address it. Jews are highly stereotyped in movies, no question, but they’re not alone in that category. I think the stereotype has actually evolved over the years. Jews aren’t the model minority anymore. That role has been passed to Asians in my opinion. Your current movie Jew is a dork but not necessarily a bookish intellectual. You can argue Seth Rogen or the guys in Harold and Kumar aren’t the most positive role models, but they’re also more like regular people and not ivory tower intellectuals or bankers.