First off, I've noticed that there are more than a few people out there who are confused as to why there are so many alternate versions of Negima.
Why do some people put a question mark in the name? Did Asuna actually die? What are Armour cards?
To clarify, here's a shoddy little page that briefly describes what each one is and where it fits into the Negima spectrum.
ネギま! Mahou Sensei Negima!
The original and by far the best version of Negima out there, written by Ken Akamatsu. While most people shrug it off as another harem manga, it is more of a Magical/Shonen piece that adds enough ecchi in it to push the line for some people, and please amuse the rest of us. 10 year old Negi Springfield is sent to Japan's Mahora Academy as part of his secret wizard training, but all sorts of crud happens that basically gains Negi a female army of magical partners and sees him off to all sorts of places in search of his missing father, the legendary Thousand Master. Ongoing.
Negima! Magister Negi Magi
The first animated attempt at Negima, created by studio Xebec. Many fans were peeved that the show's animation paled in comparison to the original manga artwork, and the characters in the show often sported different coloured hair and eyes to the manga covers. This show pretty much follows the normal storyline up until the Kyoto Arc, where several key differences come into play and leave everyone going "'teh heck?"
In this storyline, Asuna dies soon after returning from Kyoto. Then the class goes back in time to save her (Yes, with the Casseopeia, although it isn't explained) and he ends up making a pactio with everyone in the class. P.S - Satsuki's pactio ability to cook food really fast, and magical anti-demon food at that? I hope Akamatsu doesn't use this ridiculous artifact in the manga...
Negima!? Magister Negi Magi
This is the exclamation mark one. A completely different twist on the Negima plot, with Negi's drive to unmask the mysterious Black Rose Baron being his main goal in the series, aided by his usual cast of cute ministras. However instead of seeing our regular artifacts like Sica Shishikushiro and others, studio SHAFT decides to spin everyone out with the addition of a Pactio Card Chance system. Basically, Negi invokes his contracts and has the chance to draw three different kinds of Pactio Card - Dud card (Suka form) Cosplay Card and Armour Card. Aside from the trippy gag inserts and strange unexplained animals popping up in various scenes, this show is okay. Well, in any case I enjoyed it because I'm a KonoSetsu fan and the pairing is emphasised a bit more in this Negima. Also, this show is vastly similar to the manga Negima! Neo, another alternate story.
To people who wish to keep up with the latest spoilers/news about the original manga: Astronerdboy's blog and MangaHelpers are the two major places to familiarise yourself with folks.