There are a number of utilities that I'm continually using on different sites. These include:
Notepad2
Florian Balmer's brilliant, light-footprint notepad replacement. Current versions may be obtained directly from http://www.flos-freeware.ch/notepad2.html
Notepad2_04.02_64a or Notepad2_04.02_86a
Agent Ransack
Mythicsoft's windows search replacement utility.
http://www.mythicsoft.com/filelocatorlite/
MDT Administrator
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
http://sourceforge.net/projects/swissfileknife/
7-zip
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.
Libre Office
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.
http://www.libreoffice.org/download/
RegShot
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.
http://sourceforge.net/projects/regshot/
Procmon
Sysinternals Procmon is the single most important tool for troubleshooting application package issues.
http://technet.microsoft.com/en-us/sysinternals/bb896645.aspx
Portable Apps
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
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.
http://installsite.org/files/iswi/RegSpy2.zip
Explorer++
Explorer++ is a free multi-tab file manager for Windows that can be used with WinPE
http://www.explorerplusplus.com/
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.