graphics programs

• inkscape (vector art editor)
• the gimp (bitmap art editor)
• xfig (classic vector art editor)

office programs

• openoffice.org (replaces the usual Office)
• LaTeX (TeX Live distribution, see more LaTeX stuff below)

LaTeX

• simple tutorial (with PAL and others)

programming

• eclipse (development environment)
• vim (powerful text editor)

math/science

• staden (GUI sequence editor, replaces Sequencher)
• phred, phrap, consed (powerful sequence editor)
• R (statistical analysis)
• scilab (like matlab)
• octave (i use it for linear algebra)