I use my MacBook as my "command center", connecting to the other machines I need to work on using ssh and Nx. After a bit of tuning, I had this working nicely under Tiger.
Enter Leopard. I upgraded my machine rather than a clean install --- I'm in the middle of too many things to start from zero. Being cautious, I waited a few days to see what kind of issues might arise (such as the Blue Screen of Death). For the most part, the upgrade went well, with a few exceptions:
My crontab disappeared. Well not entirely as the crontab still existed in /var/cron/tabs, but running crontab -l showed nothing. To fix I just ran crontab -e and pasted the contents into the empty editor (Vim of course) and saved it.
All my printer definitions disappeared. All I have is remote printers hanging off a Linux box so this was worth a bunch of fiddling around to get things working again
AFP doesn't work with Linux netatalk. Apparently Leopard doesn't allow clear text passwords (a good thing) but the versions of netatalk on Ubuntu and Debian don't support encryption. You can build it yourself, but this will break AppleTalk printing (which of course I'm using). No more AFP connections for now.
GPG support in Apple Mail broke (requires an update from the GPGMail guys)
After finally patching up X11 in Tiger, Apple decided to ship Leopard with X.Org rather than XFree86. A total disaster. I have nothing against X.Org -- I use it on Linux -- but the implementation in Leopard is rife with problems. Take a look at the Mac forums and you'll see what I mean. While I was finally able to get an Nx session, there were scrolling problems, the yellow mouse pointer is back, and it crashed when running QGIS. I finally removed X11 and installed the XFree86 version from my Tiger disk to get things working again.
I also found a number of applications that needed to be upgraded in order to work (no surprise really). Fortunately most of the open source developers are on top of the changes needed.
Your average user probably won't have to face these issues. If you're a developer or heavy open source user, be aware it may take a while to sort out the issues with your upgrade. I just hope there aren't many more surprises lurking for me under the hood...