so we are stuck with this closed source system that keeps on adding folders to one directory, and it's going to hit the 32k limit soon because it's ext3. and that folder is expected to have +100k folders very soon too.
it's 2.6.24-27-xen x86_64 Ubuntu 8.04.4 LTS
ext4 isn't supported, reiserfs is problematic, we're now trying xfs. is there anyone that can suggest us the best way forward (ideally from experience) given the constants above ?
Go ahead with XFS. It will work just fine for you.
I have XFS in use at various busy servers. For example couple of spam filtering servers do quarantine spam to a single directory. That dir contains typically around 500 000 files.
XFS has its drawbacks, too. Mainly the delete performance is not stellar, should you need to remove lots of small files. This has been vastly improved in kernel 2.6.38 with the new delaylog option. And if your workload is metadata intensive, make sure you have lazy-count=1 option in use while you mkfs.xfs your filesystem.
Also the data corruption fears you probably have heard over the years are possible but are just as dangerous as ext3 with data=writeback mode -- a sudden server failure could lead to corruption of the files that were modified at that point. I have not personally experienced that.