The first season was only fully plotted for 13 hours, because the producers weren't guaranteed a full season. When the series was given a full 24 episodes, new plotlines were drawn up for the rest of the 24 hours (including Victor Drazen - The Man Behind the Man, the reveal that Nina Myers was an enemy, and Kim's second kidnapping).
Nina Myers was originally intended to be a loyal agent, but her motivations were changed after several episodes had already been filmed with her "good" persona. The scene where Jack is ordered to shoot her at the side of the road would have been a permanent death, but this was changed to keep her alive (via the reveal that Jack had given her a flak jacket).
The most well-known example: Teri Bauer was originally supposed to survive being shot at the end of Season 1. The film crew shot three different endings: the broadcast version (where she dies), one where she is shot but pulls through, and one where she is unharmed and walks off smiling with Jack. Teri's fate was up in the air until the start of the second season, but this is a case of Executive Meddling that turned out for the best: the incident helped develop Jack Bauer as a character and firmly established 24 as a tragic series where truly Anyone Can Die.
During Season 1, Teri Bauer was going to fall asleep for a few hours. Producers insisted she remain in the show, resulting in an extended subplot where she contracts amnesia.
An early photo shoot for Day 1 featured Mia Kirshner alongside the other five leads, meaning Mandy initially was meant to have a much larger role, possibly the sixth lead, than she did.
Season 3
At one point, Joel Surnow wanted to acquire the rights to The Da Vinci Code in hopes of working it into a plotline for the show's third season, but Dan Brown rejected him. How he would have worked Jack Bauer into a story about Leonardo da Vinci, Pagan cults and Jesus' family is anyone's guess.
Gabriel Macht was originally supposed to play Chase Edmunds in the third season. However, the producers were so impressed with James Badge Dale's audition that they hired him instead, and told Macht he would get a significant role in the next season. This never materialized. Chase was also originally slated to die as a result of a botched hand-reattachment operation at the end of the season, but this was scrapped in the script stage.
Originally, Ryan Chapelle was originally going to fake his death (and come back later) as a result of Stephen Saunders' demand that he be killed. However, after the script leaked online to a message board, the script was changed to kill him off permanently.
Kim was originally supposed to be the one to kill Nina, before the logical conclusion came down that Jack should be the one to avenge Teri's death, who had more stakes and more of a dynamic relationship with, at the time, his Arch-Enemy.
Sunny Macer was originally intended to have a larger role, and to potentially have been Jack's main love interest for the season. A combination of factors — including the availability of actress Christina Chang, and the generally poor reception of Jack's romantic subplot with Kate Warner in the previous season — saw her role heavily reduced, with a lot of her intended scenes instead given to Nicole Duncan. However, the producers liked the character enough that they eventually brought her back for Season 7.
The season finale was originally meant to get the same longer, uninterrupted timeslot that the premieres for Seasons 2 and 3 got. However, the network changed their minds at a late stage and told the production team that they would still have to include room for commercial breaks, forcing them to make substantial cuts to the episode to fit it into the timeslot. The deleted scenes included:
Saunders warning Jack that Rabens almost certainly knows by now he's the last courier, and will seek to have the Cordilla virus replicated rather than releasing it.
Theresa Ortega managing to infer from Kim's evasiveness when she questions her about Saunders that he was responsible for Gael's death. In the broadcast episode, she simply seems to guess it from glancing at a computer monitor.
Michelle trying to get hold of President Palmer in order to get him to pardon Tony for his letting Saunders escape, but not being able to do so because he and Wayne are dealing with the deaths of Sherry and Julia.
A helicopter landing on the roof of the school to evacuate Rabens, adding more urgency to the need to capture him.
Adam being informed that his sister has entered the terminal stage of the virus, and leaving CTU to be with her in her final moments.
Season 4
Chloe's exit was originally supposed to be permanent, so as to allow Mary Lynn Rajskub to become a main cast member on the U.S. version of The Sketch Show. When that series was cancelled after only four episodes, the producers of 24 quickly offered Rajskub her old role back, in part because they liked Chloe's chemistry with Edgar, and partly because they didn't think Sarah Gavin was working out as a replacement character.
Season 5
Mandy was supposed to show up in Season 5, but ended up being removed from the narrative. It's believed she would have been the assassin who kills Palmer in his hotel room (replaced by a male assailant). Additionally, the producers went through two different male actors for the role of Conrad Haas (the assassin) in the premiere before settling on Jeff Kober, as at one of the previous actors who played the character was "too young". The 24 TCG shows a different actor on the trading card of Conrad Haas, likely one of the original actors to play the role.
A well-known example: Glenn Morshower (Agent Aaron Pierce) was originally slated to die in the fifth season, but he blew the producers away with his ad-libbed response of "Is there anything else, Charles?" during a pivotal scene with President Logan late in the season. The writers hastily changed the scripts to keep him alive.
It's almost a Running Gag the number of times Carlos Bernard managed to talk his way out of being killed off. There were at least four serious bids to kill Tony (when he was shot in the neck in Season 3, when Mandy detonated the car bomb in Season 4 [which, once it was decided that he would survive, was planned lead instead to Michelle's death, suicide from grief], when the second car bomb went off in Season 5, and when Christopher Henderson stabbed him with the syringe in Season 5). Ironically, the only one of these he did not object to, feeling it was a fitting end to the character that supplemented Jack's character arc, was later Retconned.
The Season 6 DVD commentaries reveal that Josh was intended to be Jack's son, but it was changed at the last minute — apparently because the writers realized that the only way this would make sense would be if Jack had cheated on Teri while Kim was young, and really didn't like the resulting implications — to have Josh be Philip Bauer's son instead. Philip was originally going to reveal this to Josh when they were on the oil rig, but it was scrapped because it would have added too much to an already-dramatic situation.
According to various sources, Tony was at one point intended to make an appearance in the sixth season finale. It got as far along as the planning stages, with various scenarios being rumored (one would have had Tony get a separate scene after Jack walks out of Heller's house, and another would have had him confront Jack either in the finale or a DVD-exclusive scene). Either way, it never got far enough along to be scripted and filmed, although it likely would have been a better surprise than the reveal in the Season 7 trailer (for a season that was delayed for a year because of the WGA Writer's Strike, leaving fans up in the air).
Season 6's Darren McCarthy was initially cast as Eddie Izzard, but she was forced to cancel due to scheduling reasons.
The writers considered bringing back a past character to take over as CTU director for the final few episodes of Season 6, hence the frequent references Nadia Yassir makes to the imminent arrival of the new director. For whatever reason — some sources say the writers wanted to bring back Adam Kaufman from Season 3, which fell through due to Zachary Quinto being busy working on Heroes — this was dropped in favor of leaving Nadia in charge for the rest of the season, with the writers later saying that in their minds, Nadia's temporary appointment was eventually made permanent.
