Here's my situation;
I'm the lead web designer for a web site that serves as a communications hub for a non-profit spanning 3 US States (WV, OH, and PA). We are currently planning for a major re-organization where our user base will be increasing from about 400 to around 1000. Also, our admin toolbox has approx. 100 pages each with View / Update / Delete Permissions (plus a few variations which add levels to view and update).
Our current system;
uses a combination of BaseGroups and SubGroups. BaseGroups being high-level roles such as 'Admin', 'Key', 'Appointed', 'User'. And SubGroups granting low-level admin access to specific areas such as 'News', 'Events', etc. We have been plagued with short comings with this system as it's not very fine-grained. This, combined with the much larger user base, has lead us to looking for a hierarchical permissions system where permissions can be inherited down from higher levels.
That would make it a 1000x1 matrix physical. Logically, it would still be 1000x300. Also, database normalization is very key to us (which CSVs break)