- Perl. This was at the time when the other languages available to me as a student were Java or C (mid to late 90s). Those were fine, but Perl definitely felt 10x more productive for me for the things I actually wanted to write. Plus CPAN was the first directory of libraries/modules that I'd encountered of its ilk.
- VMWare/virtualization. We used it for an Operating Systems class so we could learn by actually writing Linux kernel code and running it on a VM. This was huge at the time. Friends at other schools taking Operating Systems had to work on dumbed down simulations and "teaching" OSes. Before VMWare, if you wanted to work on the kernel, you had to have spare hardware and a lot of patience for re-building your system when you did something stupid. With VMWare, you could just restore from a good snapshot and try again.
- apt-get. Coming to Debian from (old, pre-yum) Redhat, being able to type a command and reliably install pretty much anything was a huge improvement over untangling RPM dependencies. Even RPMs were a pretty big improvement over manual compiling or Windows-style installer wizards.
- Numpy (or "Numeric" as it was called at the time). Vector math in clean Python that was mind-blowingly efficient. The only other option that really balanced performance and high level accessibility was MATLAB, but that wasn't suitable for using in an application.