If what you have are mainly large flat folders with many items in (archival, that don't change often), rather than many nested folders with smaller amounts in, then a simple option for a reasonable level of data integrity is to use QuickPar to make a few repair blocks for the fileset in each folder. That way you'll get an MD5 integrity check for every file that you can test from time to time, and a way of repairing a couple of bit errors if you ever find any. One repair block can be as little as 1/32768 of the total data size, so you won't lose a whole lot of disk space adding some repair capability.

The only catch with QuickPar (at least back when I was involved with it and writing my own version) is that it will not scan and verify whole folder trees, only single folders. This is not a limitaiton of the PAR2 standard, but was a deliberate limitation in QuickPar that ignores folder information in the filenames and removes it if found. A long time ago I began my own full Assembler version that could do whole folder trees, but got sidetracked badly. It's still a useful idea and might have relevance to stevecs's BER discussion anyway, so I'll try and pick up the thread of that.