Should I be concerned about internet security having installed Quicksilver, Evernote type programs which have access to the system and can be used to auto launch by possible malicious incoming coding?

Should I be concerned about internet security having installed Quicksilver, Evernote type programs which have access to the system and can be used to auto launch by possible malicious incoming coding?

With my limited knowledge, I've taken the common sense approach in understanding I have granted these type programs some deep level of permissions to root throughout the file system placing their little programs inside to perform all sorts of wonderful tasks. Many of these programs have scriptable items which can delete files, etc.. They also require access through the firewalls (and little snitch) to perform at their best.

I noticed recently while surfing with Safari, that my browser and other functions would go haywire and a slew of ads and new windows would open. I did recently also change to openDNS as the server too. I could see that somehow these pages were actually trying to subvert me from deleting by minimizing instead of close (and quit) on hitting the normal red close button. The command menu would lite up like it was being auto functioned.

I spent an hour or so using little snitch to deny each ad type address that would install a window "under" the current open window. I noticed too that later a new address would be now associated with the page to launch these windows. I guess they have noted a block and are already setup to respaawn through different web address which would have me then create a deny rule for then that name too. My little snitch safari rules is now a page long to prevent unsolicited sites to launch under the site I am visiting.

At one point Evernote did launch on its own and place an ad in my notes.