Quadratic Forms Software (C++/Magma, SAGE)
Answers the question "What numbers are represented by a positive definite integer-valued quadratic form in 4 variables?"
PDF2DJ (Bash, Python)
A simple PDF to DJVU converter.
iPhoto AVI Video Import Crash Fix
I had trouble with importing videos from my Canon Powershot 800 IS into iPhoto. I tried upgrading to iLife '08, but is still crashed on every video. Others have reported similar problems, which were fixed for me when I moved the /Library/Quicktime/AviImporter-r7  (Intel).component elsewhere and rebooted. I hope Apple fixes this problem soon! (Added 8/28/2007)
Setup of Python mode in Emacs
I had some trouble setting up emacs (on the command line) in OS 10.4 to recognize Python files, so here are the steps I followed.
  1. Make a folder "~/emacs" in your home directory to put your emacs configuration files.
  2. Download the python-mode files from here, and untar them into the newly created "~/emacs" folder. This should create a folder named "python-mode-1.0.0".
  3. Open the file "~/.emacs.el" and add the following text:

    ;; Set my default load-path
    (setq load-path (append '("~/emacs") load-path))

    ;; To make only spaces from the tab character (useful for python)
    (setq tab-width 4)

    ;; To setup Python mode
    (setq load-path (append '("~/emacs/python-mode-1.0") load-path))
    (setq auto-mode-alist (cons '("\\.py$" . python-mode) auto-mode-alist))
    (setq interpreter-mode-alist (cons '("python" . python-mode) interpreter-mode-alist))
    (autoload 'python-mode "python-mode" "Python editing mode." t)

    ;; For colored syntax highlighting
    (global-font-lock-mode t)
    (setq font-lock-maximum-decoration t)

One can also use Aquamacs from the command line (though it launches in a new window). To do this, install Aquamacs and make an alias by adding

alias aquamacs='open -a /Applications/Aquamacs\ Emacs.app/'

to your "~/.bashrc" file (if you're using the bash shell). I like it's color scheme better than python-mode.el, but the drawback is that it cannot be run completely within a terminal. (Added 12/2/2007)