Ubuntu has come a long way in the past few years. I've been using it as my only desktop OS since Hoary, and it's come along in leaps and bounds. There are however a number of things that just seem to be "missing".
This list is a set of GUI apps that I have discovered to be missing, either on my own desktop (1, 2, 3, and 5) or while installing Ubuntu for friends (4).
#1. A Mouse Button Configuration UI
This seems like such a glaring omission that I'm baffled it's still the case. I have a mouse with extra buttons beyond the standard 3 + scrollwheel. At least 3 of these extra buttons do nothing.
However, if you go to to the Mouse preferences in the UI there is no way to map those buttons to any behaviour, in fact a Google search brings you to this wiki page: https://help.ubuntu.com/community/ManyButtonsMouseHowto
Every single part of the document describes running terminal commands, installing extra programs or editing hidden configuration files. This is a big FAIL. Just give us a UI that says, "Map button 5 to 'Back'" and I'll be happy.
#2. A Joystick/Joypad Calibration Utility
This is pretty much the same as above, but for the often forgotten about extra input device. Unlike the Mouse, we don't even have an entry under preferences for this. How can Ubuntu become a decent gaming platform when we can't even test or configure a Joypad?
#3. A Simple Painting App
Ubuntu has plenty of "photo" applications, we now have Shotwell or whatever. But occasionally you just want to scribble something on top of a screenshot, or entertain a visiting nephew. Windows has had MS Paint since, what 3.1?
There are plenty of MS Paint clones out there, pick one, shove it under accessories and let people scribble to their hearts content from the LiveCD.
#4. An iPod/iPhone Firmware Updater
This one is debatable, but simply put, Rhythmbox can manage the music but it can't reset or update the firmware (like iTunes can). You want to convert people to Ubuntu? iTunes is the big gaping hole, and although Rhythmbox + Ubuntu One does plug some of that gap, there isn't enough support for managing the other features of their iPods.
Gtkpod is OK, it does allow you to reset an iPod but again you can't update the firmware from it. Of course, the catch-22 is a firmware update could render any iPod integration unusable, but we could surely come up with a UI that only flags "safe" updates.
#5. An Easy to Use Task Scheduler
This one actually sprang up because I kept forgetting to sign into Empathy at work. Empathy doesn't start up by default so I went to find the "Start on login" checkbox only to find it doesn't exist.
There is a "Startup Applications" section under preferences, but unless your application has thought to put an entry there, getting it to work isn't exactly user friendly.
What we need is a UI that says "Start X, Y minutes after Z" where X is an application, Y is a number, and Z is Login, Network Connected, USB key inserted etc. and also cron-style "Start X at Y on Z".