My typical configuration on Bunsen labs/Debian

(just a fast track to my own reinstallations)
 
Various applications

apt-get install meld git baobab keepassx graphviz imagemagick

meld: file comparisons
baobab: disk utilization
keepassx: password maintenance utility
graphviz: automatic visualizatior for graphs, trees, etc. 
imagemagick : image manipulation tools 

Others (to be downloaded from their site):

anaconda: python development enviroment with scientific libraries
pycharm: python IDE from JetBrains
mendeley: bibliography management

My own scripts

I install them by running this command to be run in ~/bin

wget https://gist.githubusercontent.com/s1l3n0/81a5d947398306fff470/raw/e9dd25e634e912ab85c5caffe3b3339a774ef740/gitpull
wget https://gist.githubusercontent.com/s1l3n0/16880fcdc69639a40d68/raw/5eefbcbd457b6c0335f65cb4b584cf55cca8a5d7/gitpush
wget https://gist.githubusercontent.com/s1l3n0/b4be7dc6c92ad218c63a/raw/aa519ef8ef35296a72a5308eeaa1c4c0bc50cce9/findgrep
chmod +x gitpull
chmod +x gitpush
chmod +x findgrep

gitpull, gitpush: short hands for full pull/push
findgrep: look for a text recursively on all files starting from ./


Oracle Java 8

sudo -i
echo "deb http://ppa.launchpad.net/webupd8team/java/ubuntu xenial main" | tee /etc/apt/sources.list.d/webupd8team-java.list
echo "deb-src http://ppa.launchpad.net/webupd8team/java/ubuntu xenial main" | tee -a /etc/apt/sources.list.d/webupd8team-java.list
apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys EEA14886
apt-get update
apt-get install oracle-java8-installer

source: http://www.webupd8.org/2014/03/how-to-install-oracle-java-8-in-debian.html