I upgraded to Ubuntu 9.04 from 8.10 over the weekend.
The good:
Faster boot up. (worth the upgrade all by itself)
New notification “bubbles” that appear and then disappear again without any fuss.
OpenOffice 3.0 and other software upgrades.

The Bad:
Required tweaks to my pam_mount.conf.xml file to get my encrypted home directory to work. (Not an issue for most users.)

Bluetooth communication ports (serial over bluetooth) started giving errors because standard users no longer had permissions to use them. Adding the following code to an /etc/udev/rules.d/rfcomm.rules file allowed all users in the “dialout” group to access the /dev/rfcommXXX serial over bluetooth ports. (Ubuntu developers know about this problem and it will be fixed eventually.)

KERNEL=="rfcomm*", GROUP="dialout"

Java support for MIDI music failed until I installed timidity again with the following command:
sudo apt-get install timidity pmidi

The Annoying:
The hardware buttons on my thinkpad (brightness, volume, etc) still work, but no longer have an on screen display. I could fix this by installing the tpb (thinkPadButtons) package, but it takes up extra CPU cycles and power. I found that the packagers are actively discussing this issue and have decided to wait until they fix the issue within the default packages.

When running Pidgin (IM client), an “envelope” icon appears inside a “indicator-applet 0.1” to show that it’s running. Of course, Pidgin itself pops up another icon to show that it’s running on my gnome panel at the same time. I’ve thought about removing the indicator-applet from my panel to remove the duplicate items, but worried about what else I may miss if it’s not there to “hold all of the system indicators”. I eventually decided to go into the Pidgin preferences and select “Show System Tray Icon” only “on unread messages” which mostly fixed this annoyance, although now I need two button clicks to bring the IM window to the top instead of just one.

The ATI M6 graphics processor on my IBM X31 laptop was not automatically configured to use hardware acceleration. To use ppracer and other applications that require hardware acelleration to work well (such as the new version of lyx!) I had to edit my xorg.conf file following directions I found here.