We have seen, especially with XP, less with W7, that installed devices, not the ones with drivers that come built into W7, the ones you have to use Windows Update or download from the manufacturer web site, that when not present can slow apps down, in particular, apps that use those devices, like a printer for instance with Word.
Even if the main app isn't open, if a job is queued for a printer, the spooler will be looking for the printer. The spooler or other jobs like the ink-supply monitor may be looking for it too.
Similarly, if you have an MFD (multi function device), such as a printer/scanner, any manufacturer's app to support scanning may be looking for the device. HP's scan software is really bad with this. We find that Windows scan works as well. HP might get you OCR and other image manipulation SW but I avoid that if at all possible. Use the most minimum driver you can find.
If your external HDD is used to shadow the main drive and if the external drive isn't there, something may still be looking for it to be connected. Maybe not constantly, but consistantly.