Judging by the ratio of upvotes to answers, this seems like a topic that a lot of people are interested in but nobody knows about.
Personally, as a user of Ubuntu, I never use the Ubuntu Software Centre - not even for free software - I much prefer apt-get, and I'm not aware of anything (aside from paid software, which I didn't even know about until you mentioned this) that Ubuntu Software Centre does that apt-get doesn't.
As a side note, aptitude is a superior package management tool to apt-get. The syntax is the same, but aptitude has 3 main advantages:
1) Keeps track of system state. Tracks packages installed as dependencies, and remove them when necessary meaning no orphaned packages.
2) Handles recommends well. apt-get fails to handle recommends, which many packages depend on to pull in dependencies.
3) Searching. More intuitive and better formatted than apt-cache search. There is also the text UI when running aptitude directly. For example, how do I find all installed python packages?
$ apt-cache search python
Returns all packages with python in title or description.
vs
$ aptitude search '~ipython'
or
$ aptitude search python | grep ^i # installed packages are flagged with i on the first line
"apt-cache search" does AND search over everything by default which is neat to find software for something. with aptitude you have to use some cryptic flags for that.
to look for packages that you have installed use "dpkg -l"
aptitude is otherwise great and I prefer it over apt-get
With aptitude you would use the description flag (~d) like so:
$ aptitude search '~dautojump'
p autojump - shell extension to jump to frequently used directories
p jumpapplet - autojump notification icon, to jump to frequently used directories
"and remove them when necessary meaning no orphaned packages."
I understand the reasoning in this, the only downside is that it means if I've started to use something that only got installed as a dependency, it can disappear without warning.
"More intuitive and better formatted than apt-cache search."
This is neat, I may start using it.
To be honest, a lot of people have recommended aptitude to me over the years, but I've never seen enough of a benefit to try to override my muscle memory. I guess it's a classic "bicycle problem".
Although aptitude still has some bugs on bi(/multi)-arch machines, i.e. you install x64 on your machine but still install some packages in x86 for compatibility reasons; aptitude sometimes has dependency issues.
It's not a bug, but it is a problem. Aptitude's resolver is pickier. Debian has finally embraced multiarch systems and restructured x86 packages. It can still lead to weird dependency issues (but they're just that—issues with dependencies), but they're far less common and this strategy seems to have given them the confidence to include a lot more x86 library coverage than there once was.
I find Arch Linux's pacman/AUR far better than apt-get or Aptitude. Apt is all over the place - apt-get, dpkg, and building from source is just another story.
I'm a long time Debian user and always use apt-get, but I just used the USS for the first time to buy Sword & Sworcery to have something to play for the holiday. Painless purchase and one click installation.
Chose that game after seeing it in the Steam client, but wasn't able to buy it for Linux there.
Command Line is without any doubt superior than Ubuntu Software Center but I have slowly started moving all software installation and update related stuff to Ubuntu Software Center and System updater respectively. Ubuntu Software center is at the moment a little clunky.
It provides a point-and-click way to add repositories recommended by Canonical (including the paid stuff). If you're at the command line, you have to already know what repositories you want to add.
Personally, as a user of Ubuntu, I never use the Ubuntu Software Centre - not even for free software - I much prefer apt-get, and I'm not aware of anything (aside from paid software, which I didn't even know about until you mentioned this) that Ubuntu Software Centre does that apt-get doesn't.