Moving an app to the trash in most cases is alright but what you tend to find is that by doing so you leave behind settings etc. Unfortunately Apple still hasn't provided an uninstaller but have no fear there are some cool apps to do this for you.
The one I use the most is a little app called AppDelete (
http://reggie.ashworth.googlepages.com/appdelete). Simply install this then any app you want to get rid of you just drop the application onto the AppDelete icon and it moves everything to the trash, even if the app is in a folder.
It maybe that in moving Quicksilver into the trash there might be a startup app that is looking for the main app that's causing the problem. I haven't really used QuickSilver so I don't really know. Try reinstalling QuickSilver and see if that works and if the problem disappears get AppDelete and then use that to uninstall QuickSilver (the QuickSilver installer might even have an uninstaller if it's using Vise installer - it's in the drop down where it says "Easy Install" )