Wolverine
Then: Wolverine was going through some stuff. He was wearing an eyepatch and calling himself "Patch" for a little while, and then he had his Adamantium ripped out by Magneto and was just using his bone claws for a bit (which was also making him feral and crazy).
Now: Wolverine has calmed down quite a bit (or as much as he can.) These days, he's the Headmaster of the Jean Grey School for Higher Learning, and spends a lot of his time training young mutants. He's also got a couple kids (both villains), and spent some time in a black costume as part of X-Force.
Jubilee
Then: Pretty much just Wolverine's plucky young sidekick who could shoot little fireworks out of her hands. Not much to brag about.
Now: She went away for a little while, but she's back on the all-female X-Men team, and she's got an adopted kid named Shogo. Oh, and she's a vampire.
Jean Grey
Then: Wow. What a run Jean Grey had in the '90s. She was fully recovered from being possessed by the Phoenix force, she had just gotten married to Cyclops, and they had a baby daughter together named Rachel (who they believed was dead), and she was back on the X-Men's Gold team. Not too shabby.
Now: Dead. Like, dead dead. (But she does have a school named after her, which is cool.)
Cyclops
Then: See Jean Grey above. (He was also the leader of the X-Men's Blue Strike Force.)
Now: He's maybe a bad guy? It's hard to say. He also lost control of his powers after a run-in with the Phoenix force, and he sorta killed Professor X. He's now a renegade defender of mutants' rights with the Uncanny X-Men, and he's pretty much universally reviled.
Beast
Then: After spending some time with the Defenders and X-Factor, Beast had found his way back to the X-Men, where he acted as the team's genius-nerd-in-residence.
Now: Still the genius-nerd-in-residence, but has a new look. He's also responsible for bringing the original X-Men to the present day which screwed up the space-time continuum, but he's working on fixing that with his secret, illuminati-like Avengers group called the New Avengers.
Storm
Then: In the '90s, storm was all shoulder pads and little lightning bolt earrings. She actually led the Gold team, and was pretty hot and heavy with Forge from X-Factor.
Now: Since then, Storm got married to Black Panther, and became a Wakandan queen, but then they split up. Now she's back to her old '80s look with the mohawk, and she's a part of both X-Force and the all-female X-Men team, as well as Headmistress at the Jean Grey School of Higher Learning.
Iceman
Then: In the '90s, Iceman had a cool, adult look and a sweet flat top haircut made out of ice, and was part of the X-Men's Gold team.
Now: These days, Iceman is sporting some pretty gnarly spikes, and spends most of his time at the Jean Grey School For Higher Learning, where he works as a professor. He's also dating Kitty Pride.
Archangel
Then: Back in the '90s, Angel was called Archangel and had blue skin and metal wings thanks to a little run-in with Apocalypse. Luckily, he managed to keep his wits about him...
Now: ...That is, until he went insane and almost destroyed the world while working with X-Force. Psylocke was there to keep him in check (by killing him) and he lost all his memories and reverted to his regular appearance. (Except for the metal wings. He kept those.) He's now a student at the Jean Grey School of Higher Learning.
Bishop
Then: Bishop was still a brand-new character in the '90s. He was an oppressed mutant from the future who happened to find his way back to the past where he met the heroes of his time-period, Professor X and the X-Men.
Now: These days, Bishop is not in great shape. He's a maybe-ally of the X-Force, and spends his time warning the team about future threats, but he's also mentally and emotionally wrecked, and may not be totally reliable.
Colossus
Then: Reliable old Piotr Rasputin. In the '90s, Colossus spent some time on the X-Men's Gold Strike Force before going to join Excalibur with his former love, Kitty Pride.
Now: Colossus is now a fugitive after briefly controlling the Phoenix force, and has lost the ability to control the organic steel that covers his body. He's found some unlikely allies in Cable and his renegade X-Force team, and with the help of Forge, he's able to control his powers again. Also, at some point he was Juggernaut? It was pretty crazy.
Rogue
Then: A reliable member of the X-men's Blue team, with a new iconic costume and a love affair with Gambit.
Now: Still a reliable member of the all-female X-Men team, and the Avengers. That's pretty much it.
Gambit
Then: The bad boy of the X-Men, and Rogue's on-again-off-again lover. With his rakish charm and Creole accent, Gambit was definitely a fan favorite back in the '90s.
Now: He's got his own self-titled book, and even though he sees some of the X-Men every now and then, he's not a part of the team anymore.
Psylocke
Then: She spent a lot of time flirting with Cyclops (even though he was married to Jean Grey) and generally causing problems because she had just gone through a bout of body-swapping and nobody was super certain she was actually herself.
Now: Well, let's see. She died for a bit. Then she came back. Then she joined the Exiles, then the X-Force, then a DIFFERENT X-Force team. She's also been involved, and nearly killed, a bunch of dudes along the way, including Angel and Fantomex.
Morph
Then: ???
Now: ???