Your co-worker/supervisor committed a crime by breaking into your personal machines without your prior permission to do so. He also would have used methods well known already so nothing new was created or discovered.

This was not hacking (self guided learning through hands on experimentation and creation), this was a criminal act plane and simple. A real Hacker would ask your permission first and show you how it was done along with how you can protect yourself after. The mass media representation is meant to drive profits not deliver accurate information else they'd use the term criminal when what they are discussing is crime.

As for defense, the same safe computing habits you should be developing in general would also protect you against your co-worker.

- keep your software up to date; Your operating system and all the applications you install on top of it. That means Windows or osX and whatever programs have been added. The really hot targets right now are Adobe Flash, Adobe Reader (PDF files in general) and Java. At minimum, you need to confirm that the OS and those programs (if installed) are up to date.

- keep your antivirus up to date
- only install what programs you need and only if you've downloaded them from a trusted source (get your Adobe PDF Reader from Adobe not Bob's Software Download Site)
- do not open unexpected email especially from unknown sources
- do not open unexpected attachements
- do not click on links in email (hover the mouse you can at least confirm if the link displayed really points back to where it says it does)

- use a user level account with a password for day to day computer use and question why it is prompting you for administrator rights when that happens. Do not share your password with anyone (the kids can have there own accounts). Do not leave your mobile devices unattended without at least locking the screen so your password is needed before tampering with it.

The real Hackers will happily provide tips on how you can stay safe. If someone is breaking in without permission, they are not a Hacker regardless of what they or the mass media claims.