I'm also a grad student (physics) and, like you, I've figured out my own set of tools for productive science work under Linux:
Octave (MATLAB clone, super awesome!!) for crunching data and graphing
Xcircuit for drawing schematics (free as in speech)
Eagle for drawing schematics (free as in beer)
Another important task for me is automated data taking. I use Perl with GPIB modules to control programmable lab instruments. For me, this is vastly better than using LabView which is proprietary, and in my opinion damaging to the brain of any real programmer. :-)
LaTeX is utterly, completely, and totally superior to Word for technical writing. You can't make a Word document too long before you start getting all kinds of problems with graphs mysteriously jumping around, images not scaling properly, table of contents not building correctly, etc. With LaTeX you get exactly what you want and once you've had a bit of practice you can write very quickly.
I took a lab course last semester where the professor did all his handouts in Word. Most of the graphs were anti-aliased to the point that they were barely legible (bad rasterization?) and there were lots of weird formatting quirks. He had no way to generate an index for the 100-page lab manual. Me and other LaTeX-using students would hand in perfectly formatted 30 page reports with flawless graphs and schematics and he'd look on enviously...
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