Search screens, such as Constituent Search and Transaction Search, have Advanced search options that can be overriden.  

By default, the following search filters are automatically selected for all users:

Advanced search options

Search in:
Individuals Organizations Groups/Households
  Check nickname Only search primary addresses
  Check aliases Include deceased
  Check alternate lookup IDs Include inactive
  Check merged constituents Include fuzzy search on name

To change these defaults:
1.         Go into Smart Client and Design Mode
2.         Administration -> Application -> Shell Design
3.         Tasks
4.         Right-click and edit (example, Constituent Search or Transaction Search)
5.         Find FormFieldOverrides and click the ellipsis
6.         Add a new field override for the desired filter (example, INCLUDEDECEASED) with DefaultValueText equal to true or false (true indicates that the box will be checked by default; false indicates that the filter box will remain unchecked by default)