To install applications to your new ubuntu server, simply type the following (where <your application> is the name of the application you want to install:

apt-get install <your application>

For complete details on the options of apt-get, use the man apt-get command.

If, after typing apt-get install <name of appliation> you get the message:

Reading package lists... Done
Building dependency tree
Reading state information... Done
**E: Couldn't find package** <your application>

This means that either you made a typo in the name of the application, or that it is not found in one of the repositories in your sources.list. You can generate a recommended sources list (for your ubuntu server) here: http://www.ubuntu-nl.org/source-o-matic/

This will thus generate a list like the following:

# Automatically generated sources.list
# http://www.ubuntu-nl.org/source-o-matic/
#
# If you get GPG errors with this sources.list, locate the GPG key in this file
# and run these commands (where KEY is replaced with that key) 
#
# gpg --keyserver hkp://subkeys.pgp.net --recv-keys KEY
# gpg --export --armor KEY | sudo apt-key add -
#
# If you don't know what to do with this file, read
# https://help.ubuntu.com/community/Repositories/CommandLine

# Ubuntu supported packages
# GPG key: 437D05B5
deb http://us.archive.ubuntu.com/ubuntu gutsy main restricted 
deb http://us.archive.ubuntu.com/ubuntu gutsy-updates main restricted
deb http://security.ubuntu.com/ubuntu gutsy-security main restricted

# Ubuntu community supported packages
# GPG key: 437D05B5
deb http://us.archive.ubuntu.com/ubuntu gutsy universe multiverse 
deb http://us.archive.ubuntu.com/ubuntu gutsy-updates universe multiverse
deb http://security.ubuntu.com/ubuntu gutsy-security universe multiverse

Simply replace the contents (or replace using sftp or other file transfer protocol) of your /etc/apt/sources.list file with the new sources.list and then type the following after the command prompt when done:

apt-get update

Once this has been done, you can retry the apt-get install <your application> command, and if the application is in the repository, it will work.