This is a rough roadmap to the finished product, it might be missing things.

I plan on adding a lot more to this game, including 4-5 more virus fights (2 of them will be on a very big scale). The second virus is one that uses pop up ads to generate ad revenue, here is a picture of him.
The programs planned right now are Paint, CMD, Calculator, Notepad, Mail, and possibly some mini games (Pinball, Pong, something like that). The help app will be removed, and the info will be put into the Documents folder.
Parody websites are also planned, so you'll be able to browse the web. I'm not sure wether these will just be still images, or functioning sites. Obviously functioning sites would take a lot more effort, but is it worth it?
I also plan on making the antivirus upgradeable, with upgrades like faster charge time or dual cannons. The upgrades will be bought with a currency (I'm not sure what to call it) that you get after defeating a virus.
Also, the current apps will be built on, the files app will get more files to look at, the settings will have more options, things like that.
The start menu is also being remade to accomodate more apps, and a shutdown button.
Lots of easter eggs and hidden secrets are planned too!

Feel free to suggest anything you want to see in the game! I'd love to hear some new ideas. This thread is more for bigger features, if you have found a bug or want a small change then this thread might not be the place.