One of my grad students just went to remove some unwanted, automatically created files in his directory and accidentally deleted some things he wanted. I use a script to do clean ups to prevent these kinds of silly errors (which we're all prone to). Here's the script:

#!/bin/bash

if [ ! -e $HOME/.rmd ]
then mkdir $HOME/.rmd
fi

find $HOME  \\( -name '.rmd' -prune \\) -o \\
  \\( -name '*~' \\
     -o -name ',*' \\
     -o -name '#*#' \\
     -o -name '*.bak'\\
     -o -name '*.backup' -atime +5\\
     -o -name 'core'\\
  \\) \\
  -print -exec mv -f {} $HOME/.rmd \\;

find $HOME/.rmd -atime +5 -exec rm -f {} \\;

The script creates a directory called .rmd if it doesn't exist, finds files matching a certain set of patterns to that directory, and finally removes things in that directory that were moved there more than five days ago. It's not perfect--files with the same name are just moved over the top of each other.

I name it "clean" and put it in my personal bin directory. You might add or delete individual line items depending on what kinds of files your programs create. When I was a grad student, disks were expensive, and worked on a system that enforced quotas, I ran it in a cronjob once a day. Now I just run it whenever things look ugly--the same approach I have to dusting.

Building or modifying a script like this can be dangerous since a bug could cause things you care about to be systematically removed. I recommend testing it on an account that doesn't have anything you care about in it before you blindly trust it.

One last thing: I used Linux in the title, but this will obviously work in anything with bash and find including varieties of Unix and OS X. These days I'm running it on OS X rather than Ultrix or 4.3BSD. Not all versions of find have a "prune" option.