I had an unexpected experience two days ago when I deleted an application by dragging it to the trash. It's worth noting that using AppCleaner or another tool would not have helped since that app also leaves the app bundle in the trash (along with related files).
These days, it's common practice to have launch agents or daemons within the application bundle itself (the file with the ".app" extension) rather than placed in the shared ~/Library and /Library locations. Dragging such an application to the trash updated the background task management database to reference the location in the trash. I rebooted after such a deletion and the startup functionality executed from within the trash.
I've not seen this in the past, though it might have happened without any visible indication. The particular startup functionality in this case involved the display of a menu item.
I'm still researching this issue and don't know if it's a bug that the launch agent was run from within the trash.
If you really want to ensure that an application is deleted, it's best to not leave it in the trash. Finder can bypass the trash if you hold the option key down when you delete the file (i.e. cmd-option-delete).
