We probably use several hundred file organizations, if you mean file formats instead of just topographies.
The factors that I consider are deployment platform (and in some cases the availability of the server platform as well), the initial user base, the potential user base (systems either grow or die, they almost never stay "stable"), and of course the cost.
We no longer support any file formats that are intrinsically indexed. Nearly all of them support internal index structures (usually via SQL or another query language), but none that are external to the database engine.
Some indicies are relatively constant. They live as long as the underlying structure (in SQL a table) does. Others come and go according to a schedule (for example warehousing query indicies are dropped before load, then rebuilt). Still other indicies are built and destroyed on a whim (sometimes built only to support a specific user query).
-PatP