I've run tests comparing the performance of PFS3 and SFS, and PFS3 always performs better. It boots into the same Workbench setup a few seconds sooner than SFS, and takes less time to list a directory full of files.
However I have had some random errors occur with it on one machine (A1200 with DKB 1202+FPU+8MB RAM Kickstart 3.0) using two separate CF cards, one was freshly prepared and had my Workbench install extracted to it. I can't remember the exact errors now, and I haven't run a virus checker yet to confirm it wasn't simply a random virus causing the errors, but they were definitely PFS errors. I ran the PFS repair utility and it found a bunch of errors and bad files on the drive and fixed them, and I haven't seen the errors ever since.
Still, it was strange to get so many errors on a new CF card, and they were the same as I was getting on the previous card too. The next thing I'll try is switching to a different type of CF adapter, the one in there now is the model which attaches directly to the motherboard, so I'll try one that goes on the end of a short ribbon next.
These were both cheap, crap brand CF cards. On my main A1200 and on Cammy's A1200 we both have the same model 8GB SanDisk CF cards and both have Kickstart 3.1, and we have never had a single problem with our drives. All are using the Direct-SCSI version of PFS3. I've only used a 4GB and a 8GB drive in the Kickstart 3.0 machine, but only use a partition inside the first 4GB, the other equally-sized partition which was created on a KS3.1 machine is not auto-mounted, I am unsure if it will be safe to use until I get KS3.1 for that A1200 also.