Just a list of software I find useful.

Text

notepad2-mod: Replaces notepad in windows. Comes with syntax highlighting options for many popular languages.

Edit the config file to have CTRL-F5 insert date/time. Useful for keeping a diary.

Image Processing

ImageMagick: great for batch processing image files. I also use the inclued ffmpeg to generate videos from collections of bitmaps.

Fiji – It’s just imageJ, but with a load of plugins pre-installed. Very useful for analysis of images.

Gwyddion – Excellent program for analysis of scanning probe microscopy (SPM) images.

Paint.NET – Alternative to Photoshop. I find it a little easier to use than GIMP.

Utilities

Launchy: Quick access to the programs on your computer. Saves having to hunt around in the start menu.

Everything: Quickly find files on your computer. I find these days that windows find is working ok, but the indexed searching of Everything is really quick.

winscp: Securely access files on a remote computer via ssh. See post on ssh.

Pendrivelinux – Allows you to easily install Linux boot/live CDs/DVDs with a USB drive. Saves on needing to actually burn theimage to a disk.