It is probably premature of me to post my ideas, but Tycho said this was the place for them. I haven't seen any of these on the forum or its moderated counterpart.
Ransom money: Some of the time, when you wipe out a company's files, the victim company posts a reward for their safe return, no questions asked (more than what a rival will pay you to destroy them, but a small fraction of the millions that these files are worth to them). This announcement appears in the same news story that says they were lost. To claim the reward, upload copies of the files onto their file server and email an address given in the story, something like reward@Sample_Company.net. (Alternatively, all Uplink agents get the reward announcement by e-mail, as with the two competing storyline missions in the original game.)
Claiming the reward causes you to fail the original destruction mission, if there was one. You also lose Neuromancer points, because you've proven you're only destroying corporate databases for the money, not for the principle of the thing. You don't lose a lot of Neuromancer points, though, so you can copy and destroy corporate servers, fund yourself through ransom money, and become Revolutionary.
Steal an Election: There are local elections going on in different parts of the world, and corrupt candidates (or their backers) want to rig them. Your mission is to hack into the vote server, and either alter the vote totals before the polls close or upload and run a vote-switcher program before they open. You lose a Neuromancer points, because you're on the side of big money and against The People, but not too many, because your fellow hackers have already given up on politics.
When you look at the online voting server, it contains contact information for both candidates, so that the voter can make an informed choice. If you contact the clean candidate (assuming there is one), either with a copy of the virus or with the rigged vote total in advance, the other candidate gets caught stealing the election. You don't get paid this way; you get Neuromancer points (because cynics love to see a dirty politician go to jail), but not too many (because they think elections don't make a real difference).
Defend your Gateway: Some of your opponents won't merely run traces on you; they'll try to hack into Uplink's gateways and look for evidence of what you've been up to. If they get in, they'll tip off the police that there are illegal files on that gateway, and you'll have to delete all the incriminating evidence before they get there, or nuke your gateway when the cops arrive. This wouldn't happen until late in the game, when you've made some real enemies. Some of them will go so far as to delete both the driver for your gateway nuke and your file copier, plant evidence on you, or both.
You detect intruders with a monitor, prevent them from searching your files with a firewall, and prevent them from modifying your files with a proxy. These run in the background, just like your other security programs. You probably steal them from the sites you hack, but perhaps there are ways (tied to a low Neuromancer rating?) to get them from companies such as Arunmor before they go on sale.
We Have Always Been at War with Eastasia: Sometimes
truth is stranger than fiction. Either replace history on the Online Encyclopedia with a version your employer provides, or trace who rewrote it.
That Software is Not for Sale: Upgraded security software couldn't just magically appear on Uplink's site. Someone has to write it. I can think of three kinds of people who'd write programs to break security: spies, computer science professors and hippies. You might be able to get it from them before it goes on sale (but only if they trust you), you might be able to buy it directly from the source, you might need to steal it from them, and you might need to get them the data they need before they can crack a new program at all. Perhaps the higher-level bypassers and decrypters are illegal and can't ever be sold on Uplink.
No Such Agency: It's likely that the International Security Agency (or whatever it's called) will have ways to crack most or all of the security out there; the problem is taking it from them. Their supercomputer's IP would likely be in the government's internal services system. They would not, needless to say, announce when they had been hacked or what had been taken, but their response would probably be severe enough to attract media attention. In all likelihood, they wouldn't even bother to serve warrants on your bounce points; they'd just hack in themselves and look, since this is an investigation into state secrets.
Some of the other files on their supercomputer might be of great interest as well, although if they're spying on everyone, there'd be a big haystack to search.
It's for Research: A news story could announce that the government has seized a professor's research because it could be used to crack its own security, and ordered him not to publish it. You would then need to retrieve either the program itself, or a copy of the paper, which you would send to the people who gave you the mission. It would be encrypted and either on the International Academic Database, on a computer linked to from the researcher's entry in the IAD, or on the government's central mainframe. This gets you no money, big Neuromancer points and a copy of the new program to evaluate. Perhaps you can only get the mission by having either a very high Neuromancer score (so the hippies know you can be trusted) or a very low one (so the corporations know you can be bought).
The Software Liberation Front: A group of long-haired techno-anarchists who believe that property is theft, proprietary systems are evil and information wants to be free. Any resemblance to real people, living or dead, is strictly coincidental.
Very useful people to know, if you can get them to trust you (stellar Neuromancer rating), but ready to excommunicate you for the slightest infraction. They want you to release people whom they consider wrongly convicted from jail, steal proprietary engineering documents so they can reverse-engineer those products, break into the government's computers and delete patent and copyright registrations, decrypt copy-protected data and release it to the public for free, and other things of that nature. They can't pay you. What they do is write software, including illegal software that would be very useful for hacking. And, if they like you enough, they'll give it to you for free.
There might be an alternative mission tree along the lines of, "Protect our investments from these dirty hippies."
Thoughts?