

Nastier, in that it won't just show ads, install a toolbar, or use your computer as a zombie anymore. The anti-malware tools still have their place, but I'll get to that later. Security tools will help you find and remove the more obvious and well-known malware, and most likely remove all of the visible symptoms (because you can keep digging until you get that far), but they can leave little pieces behind, like a keylogger or rootkit hiding behind some new exploit that the security tool doesn't yet know how to check.

It won't be the whole infection: just a part of it. If you're infected, something from that new 1% is very likely to be one part of your infection. Mostly, that 1% is stuff that is new: the malware tools can't find it because it just came out and is using some new exploit or technique to hide itself that the tools don't know about yet. There are lots of good tools listed in answers here that can find 99% of malware, but there's always that 1% they can't find yet. Subtle malware can hide behind more obvious infections. Sneakier, not only because it's better at hiding with rootkits or EEPROM hacks, but also because it travels in packs. Here's the thing: Malware in recent years has become both sneakier and nastier:
