Up to now we have been moving feature classes to a single Enterprise Geodatabase (SDE/SQL 2012) when publishing Map Services. Are there any advantages or disadvantages in using file geodatabases?
In our shop, I find that FGDB are faster than SDE for read-only services. If you need versioning and edit tracking for services and apps, I think SDE is still the way to go. (Although, don't rule out AGOL/Portal options)
For most of our data, the masters are kept in SDE to take advantage of versioning, tracking, topology rules, etc. For services that are read only (including query or clip-n-ship), I export and redefine/format feature classes to optimize the needs for the services (I have Python scripts to aid in this). At least since maybe 10.1 or 10.2.0, the FGDBs have been faster.
Also, for raster data, mosaic datasets (may require image server extension) work better than SDE stored rasters, at least in my experience.
Tthis is not official benchmarks of any kind , but my experience .
Retrieving data ...