Links

Latex template for IISc PhD/M.Tech thesis: Click here to download (README.txt has instructions).

Freerice

Graduate School

"So long, and thanks for the Ph.D.!" A graduate school survival guide.
The PhD grind, an excellent memoir that describes what grad school is all about.
An inspiring lecture by Richard Hamming, titled "You and your research".
Blog on how to succeed in research.
Procrastination: On a lighter vein (also see this) and one with a more serious tone.

Writing:

The Chicago manual of style
Mathematical writing by Don Knuth, Tracy Larrabee and Paul Roberts.
"How to write Mathematics" is an excellent article by Paul Halmos on writing articles or papers.
Some advice on research and writing.
Henning Schulzrinne has compiled some tips for writing papers, common writing bugs, and writing reviews. Some more resources here.

Other resources:

Here are some useful resources by Richard Baraniuk.
How to learn math and physics by John Baez. Also see his advice for the young scientist.
Some musings by Micheal Steele here. Also see his advice on graduate research. It's for Statistics students, but still relevant to all.
Programming language research.
Career advice by Terry Tao. Tao has an awesome blog where he has articles on Math, and even on writing and time management.
Study hacks by Cal Newport on how to study.
Advice by Ravi Vakil.
What is it like to have an understanding of very advanced mathematics
Advice by Jason Eisner of John Hopkins University, and on How to read a technical paper
Another article on how to read a paper.
Article on how to read a paper by Micheal Mitzenmacher, and another article by Henning Schulzrinne.
This is a huge collection of advice on research, giving presentations, technical writing, job hunting, etc.
Reading for grad students by Matt Might.
A reddit post I found very interesting.
Teach yourself programming in 10 years, about expertise.
"Ten lessons I wish I had been taught" by Gian-Carlo Rota.
Taste for makers: An essay on beauty, taste, and good design.

On Teaching

A mathematician's lament by Paul Lockhart: A critique of school education.
A scathing commentary on undergraduate math education by Morris Kline: Why the professor can't teach: Mathematics and the dilemma of university education. Amazon.
Advice by John Baez.

Other links

LyX is a software based on LaTeX. It is a useful WYSIWYG (what you see is what you get) document preparation system and handy if you want to prepare professional presentations or reports but do not want to delve into the intricacies of LaTeX.

The open directory project, a useful site to search for anything technical and non technical.

An essay titled "The unreasonable effectiveness of mathematics" by Richard Hamming.

Free ebooks (legal)

A collection of classic ebooks, Project Gutenberg.
World digital math library
Digital mathematics library
Archive.org
Open library
Technical books
Another site for free ebooks.
A collection of sites.
Freely available math lecture notes hosted by AMS.

Random paper generators!

SCIgen: an automatic CS paper generator!
Randomly generate a math paper coauthored with Gauss, Euler or someone else! Mathgen
A randomly generated paper actually gets accepted at a journal! See this. One must be careful when choosing conferences/journals to submit to. Online courses and videos
Coursera is a great place to learn new areas.
So is edX and the MIT open courseware.
Tutorials in information theory and coding: SP Coding school.
Lectures delivered at the Simons institute. Also see this for more.
TCS at Princeton.
TCS plus is an ongoing online seminar series in theoretical computer science. They have some really amazing speakers.
Academic earth.
Open Yale courses.
Ars Digita university.
NPTEL: Lecture videos by professors in IIT's and IISc.
Videolectures.net.
A collection of links to online math courses.
A huge collection of online courses.

Tools

A neat tool to clean and compress scanned handwritten notes by Matt Zucker.