I use a renamer program when I get past 9999. I had one issue when my 7D decided to go back in time a few thousand clicks when it was at around 11,000 and it's only recently I have gone back in front of the original shuter count. I still have no idea what happened there, but do remember loading an old card in that had old shutter number images on it, but I don't really know. My numbering system is a bit of a mess now because of that.
But I agree, it's a major pain, especially in todays world. Back in DOS days I could understand it, as if you look at the filename there is 8 characters, which coincidently used to be the same limitations of PC filenames back in the day. Windows nowdays will handle a small story written in a filename of course. If there is one thing I'd like to see implemented in new camera firmware it's this, but if they haven't done it by now, I'm not going to hold my breath
The one I use is D-FileMU http://www.softpedia.com …Management/D-FileMU.shtml
Can be a little tricky to understand the userface at first but I find it works well. I use it to simply add a #1 in front of the number or to turn IMG_3578 into IMG_13568. It deals with batches as well of course. There may be better out there now, so if anyone has anymore, feel free to share as I'm always open to change.