i am using maverick .. and when i set proxy settings...  Systems > Preference > 
Network Proxy..
Set proxy to Manual proxy..
    example.... Http proxy: 10.0.2.2  port : 80 
   select Apply system wide to affect all... this will work already for USC..
it will write a line on /etc/apt/apt.conf
Acquire::http::Proxy "http://10.0.2.2:80";;
Acquire::ftp::Proxy "http://10.0.2.2:80";;
and so on


but problem is if you have authentication of username and password..
this will not work...because when you apply system wide... it will write still
Acquire::http::Proxy "http://10.0.2.2:80";;
Acquire::ftp::Proxy "http://10.0.2.2:80";;

with no username password..
this is a bug actually...

it should write
Acquire::http::Proxy "http://michael_c:mriddle12@10.0.2.2:80";;
Acquire::ftp::Proxy "http://michael_c:mriddle12@10.0.2.2:80";;

with michael_c as my username
and  mriddle12 as my password..

as a workaround, edit the line with this format..
Acquire::http::Proxy "http://username:password@10.0.2.2:80";;

and click save..and exit..
this will now work on apt-get  and Ubuntu software center

I figured it out while searching and noticed it when i compare it with
my two desktop that one have this when i clicked system wide  and the
other just for network proxy..

hope this will set changes in the next ubuntu release...

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https://bugs.launchpad.net/bugs/533105

Title:
  Ubuntu software center doesn't follow gnome proxy settings auth.

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