In Ubuntu 13.04, the Software Updater shows some apps as having updates, but they're non-selectable:

It's not clear why they're greyed out.

On the command line:

$ sudo apt-get upgrade
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following packages have been kept back:
  gnuplot-nox gnuplot-x11 nvidia-current
0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.

Note too that running apt-get dist-upgrade does not cause them to be installed either, as it sometimes does with packages that are kept back. Here's the output:

$ sudo apt-get dist-upgrade
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Calculating upgrade... Done
The following packages have been kept back:
  gnuplot-nox gnuplot-x11 nvidia-current
0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.

I took @quidage's suggestion, which gives the following. However subsequent upgrades show the same message:

$ sudo apt-get install -f
Reading package lists... Done
Building dependency tree       
Reading state information... Done
0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.