How can I customize/disable notification bubbles?

Is there a way you can disable or customize the notification bubbles on Lucid?

Yes you can, using a tool called Notify OSD Configuration.

If you want to disable them rename the file
/usr/share/dbus-1/services/org.freedesktop.Notifications.service:

sudo mv /usr/share/dbus-1/services/org.freedesktop.Notifications.service{,.disabled}

To re-enable:

sudo mv /usr/share/dbus-1/services/org.freedesktop.Notifications.service{.disabled,}

You need to restart your computer after either one of these changes for them to take effect.

To alter these settings, install gconf-editor from the software-center.

Scroll to / ▸ apps ▸ nm-applet and check disable-connected-notifications and disable-disconnected-notifications settings there. Check the attached image for clarifications.

As For the VLC, you need to visit VLC Preferences (Press Ctrl + P, or access it from tools Menu)

And Disable SysTray Popup when Minimized (Hover the move over that option and read the descripton)