Isolate performance-critical files in a single filesystem (or group of filesystems), suffer the storage inefficiencies there, and optimize the rest of the filesystems for storage efficiency. This solution works surprisingly well. Performance-critical files are almost always large, and storage efficiency is less critical for large files (per file wasted space is small compared to the files size).
From "Essential Windows NT System Administration" by Aeleen FrischO'Reilly & Associates, Inc. 1998
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