Unfortunately the difficulty lies in companies trying to convince you that they are the legitimate updates and, if you click on the wrong thing, it could install a virus.
If you are on a website and something pops up asking you to update, that is, almost always, unsafe. If you see an icon by your clock that wants to run an update it is usually the legitimate one.
If you are unsure and you want to update manually you can go to the appropriate sites. If you use your search to find the sites be very careful as malicious companies will try to get you to go to them.
To update Adobe Reader or Adobe Flash go to www.adobe.com To update Windows go to the Windows update in your programs. To update Java go to www.java.com