This is a growing compilation of useful software and websites I often use for my natural product related research. Feel free to suggest further interesting stuff in the comments!
Mass Spectrometry (MS)
mMass (free and open source)
Nuclear Magnetic Resonance (NMR)
ACD/NMR Processor (closed source, but free for academic use)
ACD/ChemSketch (closed source, but free for academic use)