To name a couple of obvious candidates, Perdido Street Station and City of Saints and Madmen. Accelerando might qualify as well.

Madeleine L'Engle's A Wrinkle in Time has influenced both young adult sci-fi, and countless thousands of readers and future writers. Also the first female Hugo Award Winner, James Tiptree (really a woman writing under a man's name). Lou mentioned Mary Doria Russel's Child of God. Depending on how far you want to go back, Mary Shelley's works.

Octavia Butler!! Her Xenogenesis trilogy is great. She deals with issues of race, biology, difference, and religion in this series. Also interesting is Joan Slonczewski's A Door Into Ocean--feminism, nonviolence, environmentalism--it's an interesting book. Both Butler and Slonczewski are fairly well-known among feminist literary scholars.

For more popularly taught texts in general lit courses, I second Atwood's Handmaid's Tale. Marge Piercy's Woman on the Edge of Time is great, too.

And then here are some suggestions for books I haven't read, but that are on my comps reading list (and would thus benefit from having more incentive to read): Joanna Russ's The Female Man, Joan Vinge's The Snow Queen, Sheri Tepper's The Gate to Women's Country, Marge Piercy's He, She, and It, or Zenna Henderson's Ingathering.

Finally, I'm so glad to see you guys including more women authors in the course. Yay!

I remember seeing your list a few months ago and wondering, as a thought-experiment, what my list would be. My first pass was:

* Brian W Aldiss, Non-Stop
* Isaac Asimov, Foundation
* Alfred Bester, The Stars My Destination
* Greg Bear, Eon
* Octavia E Butler, Wild Seed
* Arthur C Clarke, Childhoods End
* Thomas M Disch, Camp Concentration
* Philip K Dick, The Man in the High Castle
* William Gibson, Neuromancer
* M John Harrison, Light
* Frank Herbert, Dune
* Robert A Heinlein, Have Spacesuit - Will Travel
* Ursula K Le Guin, The Dispossessed
* Barry Malzberg, Beyond Apollo
* Ian McDonald, River of Gods
* Frederik Pohl, Man Plus
* Kim Stanley Robinson, Red Mars
* Joanna Russ, The Female Man
* Mary Shelley, Frankenstein
* Olaf Stapledon, Last and First Men
* Bruce Sterling, Distraction
* Theodore Sturgeon, More than Human
* Vernor Vinge, A Fire Upon the Deep
* H G Wells, The War of the Worlds
* Kate Wilhelm, Where Late the Sweet Birds Sang
* Gene Wolfe, The Fifth Head of Cerberus

The ones that nearly made the cut were Kress, Beggars in Spain; Slonczewski, A Door Into Ocean; Haldeman, The Forever War; Blish, A Case of Conscience.

If you're going Classic SF, then I wouldn't teach Atwood or Piercy, because they're the SF that non-SF people teach and don't have much of an idea of what is going on in the actual SF world. In short, they're genre, but they don't reflect genre sensibilities because the writers are just playing in the SF sandbox and aren't part of the larger community. McCaffrey has of course written SF, but she really writes more fantasy at the novel length.

For a short list to consider, view the James Tiptree Jr. award winners here. McHugh's China Mountain Zhang, Griffith's Ammonite, and Russell's The Sparrow are all on the list and are worthy contenders. Ironically, Tiptree herself mostly wrote at the shorter length and so unless you want to teach a book of short stories, her work might not be relevant for inclusion on your list.

I personally really like Russ's The Female Man and find it hilarious. However, I've taught it; male students (let's face it, the majority in SF classes) really, really hate it, and all students, male and female, find it dated and irrelevant, and they don't understand why Russ seems so angry. Still, in terms of impact on the genre, this has it in spades.

I am a huge Sheri S. Tepper fan, and practically any book by her is worthy of inclusion, particularly Grass, Raising the Stones, and Sideshow (which comprise her Marjorie Westriding series, though they can be read alone of course). Each of these brings up a million things to talk about with students. I don't recommend teaching her Gate to Women's Country; it's the weakest of her books, the most strident, the least subtext-y. Another good choice would be The Fresco; this is the book where fundamentalist men are impregnated by aliens, because the aliens take them at their word that "all life is sacred" and assume that their fetuses will not be aborted. Her Beauty is the best book to use if you want to focus on ecofeminism.

Joan Vinge's Snow Queen is another favorite; it has a great story, and its unfolding is riveting. This novel won a Hugo and was nominated for a Nebula.

Finally, Pamela Sargent's The Shore of Women might be another excellent choice.

Good luck! I have no idea which of these are still in print.

Tepper has tons of books, as already mentioned.
Some other possibilities:
Slonczewski's A Door into Ocean
Elgin's Native Tongue

Are you looking for feminist literature specifically or a more general 'works by women'? There are a few books in the latter category that came to my mind, but I'm not sure if they fit an academician's bill. (I work at a public library.)