Hi ieh,
this is not so much a list of my favourite apps but a way of doing a quick install for them.
what I have done is to create a "One Hit Install" terminal command, this includes all my favourite apps, some of which are listed briefly below:
synaptic: (Package Manager): https://apps.ubuntu.com/cat/applications/synaptic/
gdebi: single deb package installer: https://apps.ubuntu.com/cat/applications/precise/gdebi/
hplip-gui: (AKA: HPLIP Toolbox): a must have for HP printer owners!: http://hplipopensource.com/hplip-web/index.html
bleachbit: http://www.howtogeek.com/116971/7-tips-to-get-the-most-out-of-bleachbit-a-ccleaner-for-linux/
deluge: (a torrent downloader): https://apps.ubuntu.com/cat/applications/precise/deluge/
me-tv and kaffeine (better tuning properties than me-tv!) (DVB-T TV reception software) and linux-firmware-nonfree which is a firmware bundle for many hardware devices associated with DVB-T.
amarok: https://help.ubuntu.com/community/Amarok
Before you do the following, make sure your system is updated after your first install and that you have the "Canonical Repositories" actively marked otherwise you won't be able to install apps like "Skype"!.
If you know the EXACT name of the apps you want to install, create a list like mine, don't forget to save it and when you do a fresh install, you can quickly install all your favourite apps, create a list like the following one and copy and paste it into a terminal and then go for a cup of tea/coffee while it installs!.
My Ubuntu meta terminal command:
sudo apt-get install synaptic gdebi shutter gparted gpart xsane hplip-gui deluge pepperflashplugin-nonfree bleachbit libreoffice me-tv kaffeine linux-firmware-nonfree unetbootin devede handbrake libxine2-all-plugins transcode ubuntu-restricted-extras vamps videotrans mate-desktop-environment-extras playonlinux mono-complete p7zip-rar winbind kshisen amarok kontact skype faac flac chameleon-cursor-theme
Now just open a terminal and paste your command into to it, enter your password and wait!.
I hope this helps someone!.