The New York City Federal Reserve Bank has produced a good analysis of the changes in commuting patterns in the metropolitan area based on some recently released census data, drawing some reasonable conclusions as to why the various trends exist.

This was something that I looked at also, although not nearly as in-depth as the report. My analysis was mainly to observe the amount of long distance (or "extreme") commuting going on in the New York - New Jersey - Connecticut - Pennsylvania commuting areas. Here is the PowerPoint presentation I put together, including the GIS maps that were the main point of the project:

County Level Commute Time Mapping Using 2000 Census Data: Investigating long public transit commutes in New York, New Jersey and Pennsylvania