I like Mathematica, Magma and Maple but I use PARI-GP, Sage, Perl and GCC because they are free software.
Because I am interested in knowing low level details about computing systems I find it sometimes important to know the exact configuration of bits in data files and streams. For this reason I find hexadecimal dump programs like xxd (xxd-1.10.tar.gz) invaluable. See also a similar dump/restore program xd by John Walker at Fourmilab.
Another important detail is validating plain ASCII text files. For this reason, I wrote a "C" program "picky" to find and report on deviations from strict plain ASCII text file definition.