Some things for you to ask yourself: Do you work for a government agency? Is it possible for secret documents to be on your machine? Do you work for a high profile company? Is it possible for trade secrets to be on the machine?

What's the worst that could happen if the data is compromised? Will you die? Will you go to jail? Will your company lose millions of dollars?

> What are some good (trustworthy) tools I can scan my computer with.

There are none. Once you think your machine has been compromised the only safe course of action is to wipe and re-install, and then very carefully restore data from back-up.

Check for hardware tampering too - hardware keyboard grabbers are cheap and easy to fit.

Don't forget that burglars have different styles - they don't just rob everything. Some burglars will just steal jewellery and leave everything else; others will grab everything technical and leave everything else. And the burglars might have been disturbed in the process of robbing the house.

Any time you're infected with malware or strongly suspect you are, this is what you should do. It doesn't take that much time, plus you'll probably notice a big speed boost after you install the OS from a clean slate.

It'll take you way less time and effort than being paranoid and downloading all kinds of virus scanners and rootkit finders, while also being way more effective.

A hardware keylogger or spy device is extremely unlikely. If you don't see anything between the keyboard and the computer that shouldn't be there, odds are you're fine.

That activity could always be a decoy, of course, to throw you off the scent; or it could simply be that the thieves really were interested in those items that they took and not your computers and electronics.

There are good reasons not to take large electronics: they are not that easy to turn into cash, and they are bulky items: poor dollar to volume/weight ratio. It's much better to steal actual cash. Or traditional valuables like gold.

What's better: a computer monitor you can hawk for 50 bucks at most? Or 4 grams of gold from an 18K ring, worth some 100 bucks? Or an actual $100 bill? This is why thieves went through drawers and cabinets: they want small things that are dense with value, and cash.

As far as electronics goes, small stuff like smartphones and tables packs more value.

I wouldn't get all paranoid. One thing to do, though, is to monitor your network traffic, especially outbound, to look for any suspicious activity.

Also it could be that with a super custom and nice gaming machine, thieves didn't want it as it's too easy for you to recognize on the black market. And additionally, they might have worried you had a GPS or software which will phone home after it's been stolen.

And take a peak at the system logs too and your wi-fi logs.

Btw, a system lock won't keep any determined criminals out of your machine if they have physical access to it. Although, an encrypted drive and system locks would help, but maybe not in the case of a hardware bug.

Moderate risk - mount the both the old HDD and the new HDD (with Windows already installed) under Linux. Copy the data in Linux environment from old drive to new drive. You can use http://puppylinux.org to access Windows drives from Linux. It has a nice graphical file manager for that, so you will find it easy to do. Once done, remove the drive and store as evidence.

If something like that happened I would likely sell all the equipment and buy fresh. Really. It's pretty suspicious, and examples of malicious code which can stay persistent in practically nearly any peripheral with accessible memory have been shown.

Burglarizations suck. Hope you recover from it well.