Somebody on TWOP posted a list of Prison Break storylines that were considered but not done for one reason or another:
1. The writers considered having Kellerman let Sara escape after torturing her because he had grown fond of her, but the writers decided they had always portrayed him as a man of honor and so they wrote it as him wanting to do his duty after some struggling and Sara escaping on her own.
2. Michael, Lincoln and Sucre were supposed to go on the plane and Mahone to stop the plane from taking off with his car. Instead they wrote it as Michael and Lincoln making the intentional decision not to get on the plane (me: yeah, right, like I buy that they didn't actually HAVE to cut the scene because the plane/car scene would have been way too expensive to shoot)
3. LJ dying in a crossfire in Otis after Mahone pulls a gun on the brothers
4. Michael and Lincoln were originally supposed to come across Abruzzi, not T-Bag, in Map 1213. Abruzzi was supposed to torture the brothers to get Fibonacci's location. Didn't happen because it would be too much senseless violence with no moving the story along.
5. A young housewife in Subdivision, whose husband - a cop! - comes home with his cop buddies to play poker. The cons hit a water pipe and try to sneak out the money past the cops.
6. Sucre and Maricruz killing Hector! (These two aren't no Natural Bork Killers.) Hector beats up Maricruz after discovering that she was pregnant with Sucre's and not his baby (I never got the impression there was any reason to suspect otherwise), which results in miscarriage. Sucre finds out, scuffle ensues, Hector gets the upper hand and Maricruz shoots him to save Sucre. How very Ryan and Marissa of them. What were they smoking when they came up with this one?
7. Kellerman and Mahone old war buddies from Iraq. Michael was supposed to see a photo of the two of them side by side in their uniforms in Pam's house. Meaning nothing to him, but a shock for the audience. Discarded because it would make the already small world of Prison Break overtly incestuous.
8. Caroline pushing Terrence out of a private plane after he decided he couldn't go with the charade any longer. There was also a possibility of Kellerman witnessing this and later on informing the brothers of the body's whereabouts, which they would use to get exonerated.
9. T-Bag's hand getting really nasty during his stay with the Hollanders, almost leading to his death. But Susan, suffering from Stockholm's gets him a prosthetic. T-Bag gets close to Zack, her son, who's actually playing T-Bag. The kid uses an opportunity and runs out into the street to get help only to get run over by a car. This finally snaps Susan out of her haze.
10. C-Note taking the hospital staff who refused to help Dede hostage until they agreed to treat her.
11. Haywire successfully making it to Holland. The one in Michigan, where he's apprehended by the police and sent back to Fox River. He'd be seen talking to Larry the Dog in there, who's nothing more than a figment of his imagination. (I really like this one. Not only because of my fondness for Haywire, but because I still believe it would have been better creatively seen if at least one of the escapees ended back in Fox River.)
12. T-Bag on a killing spree in Mexico. Word begins to spread and this is how Michael finds out about his location.
13. President Reynolds' secrets getting out after a forensic test on President Mills' china prove there was poison on the rim.
14. Michael & Co ending up in prison in Mexico instead of Panama.
15. Happy ending for Mahone, who was conceived as a character with a one season long arc. He'd kill Kim and return to Pam and Cameron. The happy ending was then given to C-Note.
I guess I'm a sadist. 3 and 4 appeal to me, especially the Abruzzi one. Part of me likes the thought of Sucre and Maricruz doing Hector in, part of me realizes why it would have been a bad idea.