About this question
I'm trying to find a proper list of what standard fields are indexed by default in salesforce, as well as under what conditions custom fields are indexed.
To start things off I know fields are indexed:
When salesforce has added a custom index at your request (but you can't rely on this in other orgs)
Any fields marked as external IDs
Master-Detail fields
Lookup fields
System audit fields (CreatedDate, SystemModStamp)
I've asked salesforce support and there is no authoritative documentation on this outside of this page: http://www.salesforce.com/us/developer/docs/apexcode/Content/langCon_apex_SOQL_VLSQ.htm