Suffering from a slow connection? You get the feeling that something's bogging down your WiFi or Ethernet adapter? TCPView (also a part of Sysinternals and available via WSCC) is your chance to figure out which process is costing you how much bandwidth and deal with this connection hog. Simply launch TCPView and sort all processes by clicking the "Sent Packages/Bytes" or "Rcvd Packages/Bytes" header to get the top bandwidth hogs.
There's no better way to manage Windows boot-up than "Autoruns". This little Sysinternals gem doesn't just provide you with a better way of turning off unwanted startup entries (à la "msconfig"). It's capable of disabling scheduled tasks, drivers, codecs, gadgets, IE add-ons and more. But be careful what you uncheck: many of these drivers and services are necessary to boot your system.
15. Enhanced Mitigation Experience Toolkit 2.0
EMET strengthens security for applications without having to recompile them or waiting for the developer to release a new version. It adds several mitigations to the application of your choice, including SEHOP (Structured Error Handling Overwrite Protection), Dynamic Data Execution Prevention and mandatory ASLR (Advanced Space Layout Randomization).
Simply go to "Configure Apps" and select the ".exe" file you want to protect. Note: though I haven't experienced any problems with the applications I tested, some of these security features might interfere with certain program features (think 3rd party plug-ins that need to access the .exe regularly).
So those are my 15 favorites. What free Microsoft tools have you discovered that you can't live without?