How do you apply SET commands and other script output formatting commands to all output without running each SET command before every script?
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Settings like SET linesize, SET pagesize, SET echo and others can be stored and applied across sessions. These commands can be run when a connection is made by adding the setting commands to the glogin.sql (global login script) or login.sql files. This is a Oracle client file and is usually located at $ORACLE_HOME/sqlplus/admin directory. Glogin.sql is executes every time you start a new connection. Login.sql over rules a glogin.sql file.
You can access this directly through Toad by going to View | Options | SQL Editor | glogin.sql | Edit or ... loging.sql | Edit. These are Oracle settings files so changes to this will also affect SQL Plus output. The option to "Execute Login Scripts" and "Restore Set defaults prior to script execution" needs to be enabled.
Note: In Toad 9.0 the option is in View | Options | Execute/Compile.