1. Prepare the software you want

e.g. I download spring development tool suit

2. Make it able to run in bash

sudo ln -s ~/springsource/sts-2.6.1.RELEASE/STS /usr/bin/sts

3. Create application icon

cd /usr/share/applications
sudo vim STS.desktop

add following text:

[Desktop Entry]
Name=sts
GenericName=STS
Commen=Spring Tools Suit
Exec=/usr/bin/sts
StartupNotify=true
Terminal=false
Type=Application
Icon=/home/villim/Tools/springsource/sts-2.6.1.RELEASE/icon.xpm
Categories=Development;IDE;

4. Make application run when system startup

like tomboy, if you wanna automatically run it when system startup.just go :

System --> Preferences --> Startup Applications