Index rebuild on a large database could take longer time. One of our customer was looking for a solution to rebuild index one by one when index fragmentation is greater than 30%. Related newsgroup thread: http://social.msdn.microsoft.com/Forums/en-US/sqlkjmanageability/thread/4faae7c8-3e58-4117-8538-f397e342743f
In this blog post, I have written a SQL Powershell script that identifies indexes on tables that have fragmentation greater than 30% and performs a Index Rebuild one by one. You can also control the number of indexes to process in single script run. By this approach, you can run this SQL powershell script as a recurring scheduled SQL Agent job in non-peak hours.
You can download powershell script from rebuildIndexes.ps1
SQL agent job from Indexrebuild_agentjob.sql