A game which has a very versatile but in many ways harmless macro system is
Star Wars Galaxies, in which you can use a customized scripting language schedule actions and have one macro call on another. It allows you to automate much of your character's behavior, but there's no possibility of writing a virus or anything like what was described on the show. The problem is that it's really more helpful for gold farmers than it is for your average player.
Moving on, uploadable player content works in a particular class of MMOGs: MMOGs that are designed to be platforms for player-made content. Second Life is great with all its creative diversity, and I've seen such things as Starship Bridges and Starfleet Academy be made there, but it is often disruptive to other forms of gameplay; indeed, SL is a mess in many places. In particular, in Star Trek Online it could potentially be very disruptive to role-play.
I believe that even in-game tools like the SPORE Creature Creator could be very disruptive: It either has to be too restrictive to allow for creative designs, or versatile enough for griefers to create disruptive designs (or for people with no sense for aesthetics or Star Trek design philosophy to create real eye-sores).
One thing that might be considered for starships would be having a sort of content review committee: Now, I know people are saying it would be too big a task with all the designs coming in, but what if Cryptic (or whoever) were to charge just a small fee - say 2 USD or someting along those lines - for every suggestion? It's cheap enough that anybody who can afford to play can afford to submit a starship, but it may dissuade a lot of people from submitting designs that they know won't be accepted, not to mention that the fact that you'd have to enter credit card details and the like would give people time to reflect over their designs, so that they don't just send them as a spur of the moment thing.
Now, I'm quite skeptical towards the above idea, but an idea that I truly
do believe in is having a mission creator similar to
BioWare's Aurora Toolkit, which allows people to customize locales, items, NPCs, MOBs, dialogues, events and so forth. It's easy to use for the less computer-literate among the community, but for those who want to go the extra mile there is what's known as
NWScript, a C/Java-like coding language custom-made for the toolkit, allowing for even greater customization (indeed, the NWN community incorporated crafting into their modules long before BioWare did). Wouldn't this be great for creating Holodeck adventures?
Now, one might of course be concerned that people would create Holodeck adventures hat would be, shall we say, uncouth, and that is a valid concern. Now, what I'm suggesting is that there be some sort of Holo-Library - sort of the iTunes of Holo-novels - where people could download, rate and review Holo-adventures, and offensive ones could be reported for review. Now, because Holo-adventures would be instances, what happens in there won't disturb those who are not taking part, so you can have Constitution-class ships and dragons and what-not in there; BioWare created a good bit of content for the Aurora Toolkit that was never used in their original modules.
Now, as for destructive code: The scripting language should be such that any such code could only harm your current in-game experience, and never your machine (I believe it was Zach who put it thus: The game is like a separate operating system.). Therefore, it doesn't hurt the game terribly if somebody writes such code: People will just have to remember that they are playing strangers' Holo-adventures at their own risk.
Furthermore, you would be able to take no rewards in the form of experience points, currency or items - apart perhaps from ornamental ones, such as a plaque or some other trophy designed by the Holo-author - with you off the Holodeck, so it couldn't grant you an unfair advantage over other players; no Level 100 Machines or Wands of Inflation.
