SQL Server Management Studio – Clear Find and Replace window history

In Regedit:

For SQL Server 2005 :
HKEY_CURRENT_USER\Software\Microsoft\Microsoft SQL Server\90\Tools\Shell\Find

For SQL Server 2008 :
HKEY_CURRENT_USER\Software\Microsoft\Microsoft SQL Server\100\Tools\Shell\Find

For SQL Server 2012 :
HKEY_CURRENT_USER\Software\Microsoft\SQL Server Management Studio\11.0\Find

Remove the Find and Replace items.