Trash files in the safe mode?
Normally yes.

The safe-mode is only blocking certain features of Mac at the boot time.
See http://support.apple.com/kb/HT1564?viewlocale=en_US&amp;locale=en_US


  It loads only required kernel extensions (some of the items in
  /System/Library/Extensions).
  
  It disables all fonts other than those in /System/Library/Fonts (Mac
  OS X v10.4 or later).
  
  It moves to the Trash all font caches normally
  stored in /Library/Caches/com.apple.ATS/(uid)/ , where (uid) is a user
  ID number such as 501 (Mac OS X v10.4 or later). It disables all
  startup items and login items (Mac OS X v10.4 or later).


Eg if you have a problem with a font, a corrupt driver/kernel, ... it's possible you wont be able to use your Mac, since the Mac can crash at boot etc, booting in Safe-mode is a chance to solve those problems.