What is the best way to monitor long running queries in SQL Server?
Following Gaius post: You can create an .SQL script which does what you need with use db in front of the script -> create a SQL Agent job of Operating system type which calls the script: 

sqlcmd -E -S SERVERNAME -i"c:\YOURSCRIPT.sql" -o"C:\YOURSCRIPT_LOG.log"

Add new step and use msdb.dbo.sp_send_dbmail procedure to send email. This feature can be customized to display inside the mail a specific query from SQL tables to confirm the execution of the script... for example dbcc showcontig of your rebuild indexes.