A service file typically contains records of the soldier's military service, including enlistment, promotions, transfers, discharge, and the soldier's presence or absence on paydays, among other things.  Although the contents of a service file is usually military in nature, it may contain some biographical or genealogical information.  For more details about the typical contents of a service file, see this page.
A pension file typically contains documentation of the soldier's military service insofar as is necessary for him to qualify for a military pension. The file may also contain copious medical records to document the soldier's disability, if any. Many pension files also contain lots of biographical and genealogical information, especially in the case that the applicant is a widow or other dependent as they would be required to prove their relationship to the soldier.  For more details about the typical contents of a pension file, see this page.
Although the focus of these two files is different, they can both contain very useful information for researchers.  It is therefore prudent to obtain copies of both files whenever possible.