If you go to the ISTS support site (rather than the forum) you can purchase a nice multi-file re-index utility rather than sitting there for a few hours selecting one file at a time.
 
And it is very inexpensive.

Generally only if you are having a problem and getting error messages.  The other time is when you purge data or consolidate transaction files.  The disk space from the cleared files is not recovered until they are reindexed.  So for example, if you archived a bunch of Work Orders to the Work Order History files, you would want to reindex the active work order files to reclaim the disk space.