Recommended

Below is a list of books, blogs, websites, services, software, ... that I personally recommended. Note that some of the links are affiliate links.

Software

Below is all software that I install when I get a new pc.

Windows Utilities

SlickRun : Starts programs quickly but what I especially like is hitting Win+j which pops up a small note taking utility that I use as a longer term clipboard.
Fences: Organize your desktop icons with the added bonus to hide them in one double click (e.g. before giving a presentation).
PureText: Paste your clipboard content as simple text, it removes all markup which can be great when pasting text into an e-mail or document.
Karen's Replicator: Keep multiple folders in sync with a schedule. I use it for creating a backup of my work drive to a server.
KeePass: Password manager, if you're using Chrome I can also recommend using the Chrome extension chromeIPass.
f.lux: Automatically adjusts the colors of your monitor during the day to prevent eye fatigue.
7-zip: The best open source file archiver with a high compression ratio.
Chocolatey: apt-get for Windows. Use it to install Putty with the command 'cinst putty'.
BareTail
BareGrep

Development

Notepad++
Visual Studio + ReSharper
R + RStudio
Fiddler
Python + SciPy

GIS

OSGeo4W
Quantum GIS
gdal

Chrome extensions

pocket: In one click saving an url to read on my phone.
chromeIPass: Never forget a safe password.
StayFocusd: Block procrastination websites while working.
AdBlock: Block excessive ads.
Tab Outliner: Crash resistant session manager, saves my life when Chrome doesn't restore my tabs after a crash.

Websites

...

Books

I might not read as much as fogus but I should start listening to his advice of keeping a record of what you've read. Below is a short selection of books I remember I've read AND that where really good.

Programming & CS

Real World Functional Programming: With Examples in F# and C# by Thomas Petricek and Jon Skeet: This book really delivers on what the title promises. It starts gently but the last chapters are more advanced and challenging. Parts of this book can be read on MSDN.
Functional JavaScript: Introducing Functional Programming with Underscore.js by Michael Fogus: an introduction to functional programming presented in JavaScript, if you're totally new to the concepts of functional programming then it won't be an easy book but it's definitely worth the effort (my review).
JavaScript: The Good Parts by Douglas Crockford (he popularized JSON and wrote JSLint and JSMin): if you develop regularly in JavaScript then this book is a must read.

Other Non-fiction

Harry Potter and the Methods of Rationality by Eliezer Yudkowsky
Culture & Empire: Digital Revolution by Pieter Hintjes: Take a look on Amazon  or read my review.
The Art of Learning by Josh Waitzkin: The title says it all, a few years ago I wrote the following notes part 1, part 2 and part 3.
The Paradox of choice: Why More Is Less by Barry Schwartz

Fiction

Some authors:
Paulo Coelho
Haruki Murakami
Sergei Lukyanenko: Night Watch, Day Watch, Twilight Watch
Jacqueline Carey:  Kushiel's Dart, Kushiel's Chosen, Kushiel's Avatar
Rob Pearce: Nanocorporate
Edwin A. Abbott: Flatland: A Romance Of Many Dimensions
Dave Eggers: The Circle
David Kirk: Musashi series
James Clavell: Shõgun