From Identity Finder technical support in answer to the question of SQL Server configuration for a 3000 IDF endpoint system:
The database is primarily bound by disk speed and secondarily bound by number of CPUs and RAM. For 3000 endpoints you'll need to make sure you are using at least SQL Server standard edition as SQL Express has too many limitations that will affect your performance. You'll want at least 2 cores (or CPUs), speed of the CPU doesn't necessarily matter, just as long as it is fairly recent (I would say, 2.0Ghz or higher).
RAM will be crucial for the database result sets. In other words, if you are going to be reporting across all of the endpoints, you'll want enough RAM to be able hold the result set into memory. Side note, if your SQL server is on a separate machine other than the IIS application server, you'll want to have at least 2GB or 4GB on that system as well.
We wouldn't recommend RAID5 for the database because it would take away from the database performance. The database is mostly bottlenecked by disk performance so having as many spindles (physical disks) as possible would greatly benefit database performance. Additionally, you'll want to make sure to have at least three separate volumes for the OS. At least one for OS itself, one for the database data, and one for the database log. It is important to note that each one of the volumes should be on separate disks (or SAN LUNs) for maximum performance.
Based on a typical amount of data found on the endpoints and for 3,000 endpoints, we think 30-60GB for the database data and about 6-12GB for the database log. The OS, doesn't need more than 30GB and 20GB should be fine.