Adaptation Displacement: To many a Studio Ghibli fan, it's fairly unknown that there even is a manga of Nausicaä. Although the movie is really just a 2-hour compression of the first quarter of the manga.
Anvilicious: Of the Green Aesop variety, mostly for the film though. It gets a bit more complicated, if not somewhat subverted towards the end of the manga. Specifically, the question of whether or not the Master Computer's plan to artificially restore Earth's old ecology is just as bad as the callous environmental destruction that preceded it, since it would mean the deaths of the countless biotechnological creatures (including "Humans") who have made a life for themselves in the new world.
Nausicaä herself is much colder and dire than in the movie, fitting for the manga's more nihilistic tone... although she still ends up largely on the side of idealism. The fact that her real opponents in the manga are full-blown Omnicidal Maniacs, Master Computers and whatnot means she also needs to have a little more steel in her will than her film counterpart ever has to muster.
Broken Base: Despite being uncut and more accurate, Disney's dub of Nausicaä still has its share of harsh detractors, with some declaring that it still fails to do justice to the original Japanese. You'll have to decide for yourself if you like it or not.
Fans tend to be split over the manga. Some consider it to be a vastly superior story to the movie; others think the plot gets too muddled and self-indulgent in the later volumes and prefer the movie's Adaptation Distillation.
Escapist Character: Nausicaä. Who wouldn't want to fly around the world in a miniature aircraft, exploring beautiful forbidden lands?
Jerkass Woobie: Possibly a number of characters, but perhaps most notably Kushana. Introduced in the film version as a seemingly stereotypical evil queen ("Nice valley. Think I'll keep it."), her status as an apparent Card-Carrying Villain is quickly subverted. This apparently was deliberate on the part of the writers: Miyazaki describes Nausicaä and Kushana as "two sides of the same coin", largely differing in that Kushana has "deep, physical wounds".
Les Yay: Nausicaa and Kushana have some of this going for them as Kushana seems to take a bit of a shine to Nausicaa as the story progresses.
Macekre: Warriors of the Wind again. The incident is why all Studio Ghibli licenses contractually stipulate that not a frame of animation is to be changed or cut (with the obvious exception of replacing the credits).
Moral Event Horizon: The Torumekians (especially Kushana and Kurotowa) cross it early on when they enslaved Peijite and assassinated Nausicaa's father. However the moment that seals them as barbaric and irredeemable warmongers is the invasion of the Peijite aircraft which was filled with children and the words that followed it:
"Leave no survivors!"
Squick: Film-only example. When Kushana takes off her glove to show that she no longer has an arm and then says "Whatever lucky man becomes my husband shall see far worse than that." Ew.
She retains the armor on both her legs after taking off her armor, too.
Note that in the original manga, Kushana appears to be 100% whole (she retains her arms and legs in any case).
Tear Jerker: Nausicaa flying straight into a Pejite flying machine, standing on her glider, her arms outstretched always makes this troper choke up. They're shooting at her and she still believes they won't kill a defenseless girl. In the world she lives in, that kind of faith in people is touching as hell.
Nausicaä realizing the Pejite are going to kill everyone in the valley, including her people, just so they can stop the Torumekians. Asbel finding his entire city is destroyed is quite sad as well.
The baby Ohmu healing Nausicaa's bullet wound (or at least taking away the pain) and her subsequent breakdown. After being tortured and used as bait by humans for their own selfish purposes, the baby has absolutely no reason to trust humans at all, even after Nausicaa prevented it from killing itself in the acid lake. Nausicaa herself sums it up perfectly: "You're so kind."
Word of Miyazaki states that Nausicaä's resurrection near the end of the movie was not meant to be analogous to Jesus and that he would have changed it if somebody had pointed out the similarities before the film came out (Miyazaki is many things, religious is not one of them). This may well explain some of the open discussion about the permanence of death (and how ways of avoiding it are explicitly unnatural) in later stages of the manga.