I had an Idea, and I doubt this will be implemented any time soon, or if it will just be an event, however it would be possible to imprison players, under the employ of certain cities, and factions. At first this became an Idea that would work simply with Vault City, a concentration camp placed somewhere nearby where players would have to mine/craft for Vault City once a player had been sent to the camp. This Idea then expanded to Enclave, NCR, and Vault City, Players could go under employ as a licensed bounty hunter/officer for each city, and hunt down other players with a rope or craftable handcuffs. I'm still tinkering with the mapper so I haven't been able to make false screenshots like Cryofluid did for his Outpost suggestion.
Safe towns and large factions reward bounty hunters/officers for hunting down subjects on a 'shit-list'(outstanding Negative Karma with that area), the players must avoid killing the target and getting them into negative health, then use a rope/handcuffs on the character, which will send them to a respawn camp that they have to work there way out of to escape or reach parole. Vault City and Enclave will not parole you, and probably have other plans for you(Vault City may want to reform you and make you a servant, while enclave will want to experiment on you) Depending on how outstanding your Karma is with good organizations(you will still be negative, and an ex-convict), you can work off your bad Karma until you are Neutral again(Still somewhat negative but they won't attack you), and reach parole, or you'll be forced to escape if your Karma is too outstanding to raise back to neutral. (meaning you're in for life if you don't escape.)
Jailbreaks can take teamwork in creating a riot, or an outstanding science skill(setting the power off or hacking electronic locks), or a mixture of both. There should be multiple ways to get out, varying from compliance with orders, bribing guards with drugs crafted in the workshop, or hiring temporary mercs with cigarettes who will help you fight your way out. You have no equipment whilst incarcerated, and you must do labor(From handling the laundry to mining ore) in order to earn cigarettes or some other form of prison currency. The perks to being imprisoned by Vault City or Slavers, is that your faction can buy you back, but some factions might not want to hand money out for weaker comrades, whilst the stronger comrades are needed for TC, PvP and Crafting.
Escape routes could include working your hide off to obtain a crowbar to get into a pre-war reservoir or sewer, or working with prison gangs to gain the resources to escape. Providing players with options depending on their skills can get them out on their own in lower security prisons, however getting out of Enclave/Brotherhood prisons will be a huge pain to escape on your own, as guards are more well armed, and the designs of Enclave/Brotherhood containment centers will be less flawed or frayed. Depending on a luck roll(And availability of Cell-mates) you may end up bunking with a useful/useless NPC or nobody at all. Useless NPC's still hold the use of being killed and looted, whilst Useful NPC's may have a plan, or they always keep an eye out for their cell-mate and provide extra muscle.
Also, you have the ability to insert jokes about dropping the soap in this area, as old as they are, lots of people still laugh at the horrible fate of being worked over by Bubba, Mad Dogg, etc.