Below are a few characters I noticed are similar to Jenova in some way or another. It may be in appearance, actions, or anything. =P The characters are from games, movies, anime, etc.

Agatha (Minority Report)
As soon as I saw Agatha in the pool at the beginning of Minority Report, I noticed that she looked a little like Jenova and was being kept in a similar way to her - Jenova lives in a tube in a nuclear reactor, while Agatha is kept trussed up in a pool in the precrime headquarters. She seems to be a very clean character, which reminded me of the image of Jenova wearing her metal mask. Also, both characters have supernatural powers: Agatha is able to forsee murders, and Jenova has the ability to exercise control over her puppets.

Tima (Metropolis)
The character of Tima reminded me a lot of Jenova, particularly since there's a scene in the film with Tima in a tube in a laboratory - just like Jenova's tube in the reactor. A screencap will appear here when I get time to watch the DVD again. Anyway, the scene with Tima opening her eyes in the tube reminded me a lot of the FMV when Sephiroth takes Jenova out of the reactor.

Kos-Mos (Xenosaga)
Although I don't know much about the character of Kos-Mos, her appearance seems quite similar to Jenova. She's also a robot, so the whole metal-mask idea also fits. Her eyes are much more vibrant than Jenova's, though, and she has longer hair - although I can sort of picture Jenova with long blue hair. You can find more info on Kos-Mos at Complexity, Annie's kickass shrine to her.

A.L. sent this suggestion:
A little (big, actually) something from Mobile Fighter G Gundam reminded me VERY much of Jenova - the Devil Gundam (i.e. Dark Gundam for Cartoon Network [curse officious censorship!]). It started off as something called the Ultimate Gundam, a fully bio-mechanical instrument with the purpose of restoring a war-torn Earth to its previous (and more habitable) state by supplementing its dwindling plant and animal life with its revolutionary nanotechnology, later termed DG cells (Sound familiar?). It has the incredible capabilities of self-recovery (hmm...), self-replication (hmmmm...), and self-evolution (HMMMMMMMM...!). There was an incident, and the Ultimate Gundam crashed to earth, making a sizable crater (though it wasn't as far north as you'd expect). The impact caused its systems to malfunction (unrelated to Jenova) and is now hell-bent on destroying the Earth (specifically, humanity, very MUCH like Jenova). Through the DG cells, it has the capability of reanimating corpses, which form a force of uncertain origin known as the Death Army (i.e. Dark Army for Cartoon Network [once again, curse officious censorship!]), which is very much like a cross between the Sephiroth-clones (zombies) and Soldier (living people who are infected experience an incredible power-boost, though they become subject to the will of the primary machine in what they apparently believe to be some sort of "enlightenment"). The Death Army (just the dead guys) are then absorbed by the Devil Gundam (sort of like the Reunion) so it can complete its evolution (I wonder if that's where they got Jenova*SYNTHESIS?). It also needs a human (pilot) for it to properly function, and near the end of the series, atop of fusing with a space colony (becoming one with the planet) it takes a girl and binds it in some sort of silver metallic shell which looks a great deal like that mechanical angel in the reactor. And did I mention it uses tentacles? Tentacles that make all sorts of really disgusting hawking/gasping/sucking noises?

Eitan & Tsvika Tsuk sent this suggestion:
Lavos from "Chrono Trriger" is also very similar to Jenova in the idea of alien, "crisis from the sky", coming upon the planet to suck it's energy.

The Enemy sent this suggestion:
Another similar character is The Borg-Queen from Star Trek: First Contact. She has her head detached from her body as she shows up first (Like sephy takes Jenova's head in nibelheim) The Queen also "controls" all borg, so, like the mind manipulating of jenova and at the end, she falls into a deadly gas. (lifestream? true jenova didn't fall into lifestream, but still.)