Sure sign of system compromise No. 7: Unexpected software installs
Unwanted and unexpected software installs are a big sign that your computer system has likely been hacked.
In the early days of malware, most programs were computer viruses, which work by modifying other legitimate programs. They did this to better hide themselves. For whatever reason, most malware programs these days are Trojans and worms, and they typically install themselves like legitimate programs. This may be because their creators are trying to walk a very thin line when the courts catch up to them. They can attempt to say something like, "But we are a legitimate software company." Oftentimes the unwanted software is legally installed by other programs, so read your license agreements. Frequently, I'll read license agreements that plainly state that they will be installing one or more other programs. Sometimes you can opt out of these other installed programs; other times you can't.
What to do: There are many free programs that show you all your installed programs and let you selectively disable them. My favorite for Windows is Autoruns. It doesn't show you every program installed but will tell you the ones that automatically start themselves when your PC is restarted. Most malware programs can be found here. The hard part is determining what is and what isn't legitimate. When in doubt, disable the unrecognized program, reboot the PC, and reenable the program only if some needed functionality is no longer working.
Sure sign of system compromise No. 8: Your mouse moves between programs and makes correct selections
If your mouse pointer moves itself while making selections that work, you've definitely been hacked. Mouse pointers often move randomly, usually due to hardware problems. But if the movements involve making the correct choices to run particular programs, malicious humans are somewhere involved.
Not as common as some of the other attacks, many hackers will break into a computer, wait for it to be idle for a long time (like after midnight), then try to steal your money. Hackers will break into bank accounts and transfer money, trade your stocks, and do all sorts of rogue actions, all designed to lighten your cash load.
What to do: If your computer "comes alive" one night, take a minute before turning it off to determine what the intruders are interested in. Don't let them rob you, but it will be useful to see what things they are looking at and trying to compromise. If you have a cellphone handy, take a few pictures to document their tasks. When it makes sense, power off the computer. Unhook it from the network (or disable the wireless router) and call in the professionals. This is the one time that you're going to need expert help.
Using another known good computer, immediately change all your other logon names and passwords. Check your bank account transaction histories, stock accounts, and so on. Consider paying for a credit-monitoring service. If you've been a victim of this attack, you have to take it seriously. Complete restore of the computer is the only option you should choose for recovery. But if you've lost any money, make sure to let the forensics team make a copy first. If you've suffered a loss, call law enforcement and file a case. You'll need this information to best recover your real money losses, if any.
Sure sign of system compromise No. 9: Your antimalware software, Task Manager, or Registry Editor is disabled and can't be restarted
This is a huge sign of malicious compromise. If you notice that your antimalware software is disabled and you didn't do it, you're probably exploited -- especially if you try to start Task Manager or Registry Editor and they won't start, start and disappear, or start in a reduced state. This is very common for malware to do.
What to do: You should really perform a complete restore because there is no telling what has happened. But if you want to try something less drastic first, research the many methods on how to restore the lost functionality (any Internet search engine will return lots of results), then restart your computer in Safe Mode and start the hard work. I say "hard work" because usually it isn't easy or quick. Often, I have to try a handful of different methods to find one that works. Precede restoring your software by getting rid of the malware program, using the methods listed above.