I've been using PFS3 since early 2001, and my opinion is mixed. Since SFS is free and still being updated (or at least it hasn't been abandoned), if I was starting today I'd use it with no hesitations. But PFS3 is a known quantity for me and I don't make changes lightly, so for now I continue with it.
Two technical downsides of PFS3:
1) Block sizes go no larger than 1024 bytes, which can be a problem on larger hard drives or on certain devices.
2) There is apparently a potential incompatibility with ixemul.library software. Or at the very least, the first version of AmiGift (file sharing software) was highly-incompatible with it until the author specifically added PFS3 support in AmiGift 2.
I had no trouble with PFS3 until 2 1/2 years ago when I mistakenly reconnected an external SCSI drive inappropriately and couldn't understand why I was suddenly getting so many hard drive errors. I ran PFSDoctor several times, and in trying to fix the problem, it deleted files everywhere! (FFS is unique among file systems in that it offers a potential lifeline for recovering mangled or deleted files. In worst-case scenerios, repairing other file systems generally means deleting files until everything gets back in sync.) Finally I realized my mistake, corrected the SCSI chain, and rescued the remainder of my partitions. Thankfully I had backups, but still lost a lot of YAM email. (From this I wrote two very crude Arexx scripts that trawl through PFS3 partitions to rescue YAM mail files.) I'm not blaming this on PFS3.
Since then, though, I've had two more implosions on my "Programs" PFS3 partition, and each time YAM appeared to be at the center. I again lost tons of mail. This latest time (October 2006), in the course of fixing the problem, PFSDoctor actually deleted my entire YAM directory! Whatever happened even followed a soft link to my "Data" partition (PFS3 supports these) and deleted some YAM files there, too!! I don't know if the problem is strictly with YAM 2.4p1, if it's a fragmentation bug in PFS3 (thousands of little mail files on the drive), or some lingering low-level problem with the drive from the SCSI incident. It could also be that the YAM crash is corrupting memory used by PFS3, so they're both slightly to blame. But it's starting to tick me off.
At the time I was running PFSDoctor once a week, to make sure these little errors weren't creeping up on me slowly, and without any warning. PFSDoctor had given the partition a clean bill of health just 3 or 4 days prior.
Since then, I've actually switched to using my ISP's webmail. It's definitely slower, but I've had no problems so far. (As my incidents have been averaging roughly once a year, that doesn't really mean anything.) When I have time, I want to backup both the "Programs" and "Data" partitions and rewrite them with a new, third partition specifically for email. I'd also like to learn the structure of PFS3, so I might see for myself one day exactly what's going wrong, and perhaps write my own backup/recovery tool.
Conclusion: PFS3 may not be at fault, but if it is, I won't be getting help from the author. I'd suggest SFS.
Hope that was helpful,
Todd