There are a number of utilities that I'm continually using on different sites. These include:
Florian Balmer's brilliant, light-footprint notepad replacement. Current versions may be obtained directly from http://www.flos-freeware.ch/notepad2.html
Mythicsoft's windows search replacement utility.
Another great example of what a community can produce. ChrisofSweden has produced a really useful HTA frontend for simplifying MDT deployments. Anyone using MDT should take the effort to look at this project.
Swiss File Knife
Probably the most over-the-top development I've ever seen. This file utility does almost everything you could think of. The list of functions may be viewed at: http://stahlworks.com/dev/swiss-file-knife.html
Without any doubt the best zip / unzip program available on the web. The utility is unique in it's ability to open MSI installers to expose files within embedded cab files.
After recently needing a license-free Excel worksheet editor I checked on the progress of the Libre Office - office suite of tools. Full support now exists for the Microsoft Office 2013 suite. Libre Office now also support all versions of Visio file format.
The best free snapshot comparison utility. Don't be deceived by the name, the utility is not limited to comparing registry changes, file changes are also recorded between snapshots.
Sysinternals Procmon is the single most important tool for troubleshooting application package issues.
An extensive collection of valuable tools and utilities that may be run from a USB key. Really helpful for WinPE or restricted Windows environments.
Regspy if a freeware alternative to the Wise Com Capture utility. It allows self-registration information from DLL files to be captured in .REG registry files.
Explorer++ is a free multi-tab file manager for Windows that can be used with WinPE
MSICheck, MSIEdit, Application Launcher
All freely available from this site
MSICheck - for checking and reporting on Windows Installer packages
MSIEdit - for quickly editing & branding Windows Installer packages
Application Launcher - for testing install and removal procedures of a package.