4nec2 - amazing tool for many antennas and really easy to use.
Octave - is nearly as good as Matlab for most things
Avago AppCAD - useful tool.
GNUradio Companion - can be used with or without hardware in the loop. A bit like Matlab simulink(but better)
Universal Radio Hacker - decode many digital modulations schemes.
AnTune - antenna matching circuit design(needs a VNA)
There must be a good Smith Chart program, but I havent found one.
OpenEMS - looks fairly powerful, but seems a bit tough to learn.