I have been using NTFS, but I recently took a drive which is normally attached to a Mac mini running Lion (using Paragon NTFS) and attached it to Windows 7 because the drive was disconnecting spontaneously. Diagnostics didn't show a problem, but I decided to go ahead and copy it to another drive anyway.
It showed up on Windows 7 and I selected the two folders to copy to another drive and nothing happened. The drive disconnected and then it lost a whole folder about 1TB - I believe it's probably still there since the space is used up, but Windows must have had some kind of problem. I reattached it to the Mac, but the stuff is gone. I don't know if it's bad filenames or a bug in Windows 7 or Paragon, or what, but this isn't the first time I've had problems with external USB drives going between platforms or external drive failures when attached to OSX.
Normally I leave them attached to only one OS, but I need to be able to move them around if I have to get to the files from another machine.
Question is more for the future - what cross-platform file system should I use for these external drives? Or should I get away from moving these things between platforms?