Theses are the tools that I am using now:
for keep in touch with my adviser, follow the assigned tasks, keep revisions of papers.
My works based on Java, Eclipse is a best IDE for me (so far)
3) Power Point
Of course, for presentation
For calculation, process simulation result data, making graph.
5) Latex and Ms Word
Last year I used MS word, but I am changing to LaTex.
LaTex is far better than MS work, for scientific paper.
If you plan to be in grad program, you should start learning it now.
My LaTex Tools are:
7) Specific Tools for me
SPSS, AMPL, Sigma Plot,
8) Monitor Management (for dual monitors and PC remote control)