Secunia emphasizes that this is to be considered as a best case scenario, as users of their tool are to be considered security aware.

From my own experience of running the tool, it is that these numbers should be taken with a grain of salt. Even though all software are up-to-date on a system, the tool still finds old files remaining but not in use – Flash tends to be a good example where a plethora of versions can be spread out on your system without being in use. It also won’t take into account whether the unpatched applications are even used anymore – they might have been installed once and just forgotten.

Sometimes updated software could mean that other software or features become incompatible, and would be another reason for not updating.

Even still, it’s always best to keep most software updated. It usually isn’t much hassle at all any longer, just a few clicks with your mouse (or a few more if on Vista with UAC). The way that software repositories in popular Linux distributions work, is really to the advantage when it comes to everyday software update checking.

(via: IDG)