Cloanto has been signing all Windows executable files ("desktop" apps) released since 1999 with Microsoft Authenticode technology. In 2014 this was extended to include dual SHA-1 and SHA-256 hashes.
When you right-click a Windows executable file (e.g. files ending in .exe, .msi or .dll) you can select Properties, and then Digital Signatures, to verify the digital signature of the file. This allows you to confirm the publisher, the signature time, and the integrity of the file. Under Details, the signer name should be "Cloanto Corporation" and the dialog should say "This digital signature is OK".
If you selected Properties/Digital Signatures on an executable file and noticed an error message, or no digital signature at all, or a digital signature not signed by Cloanto Corporation, a verified Nevada, USA, corporation, this may mean that the file is either incomplete or corrupt. This may have been caused by a download problem, or, for example, by a malicious modification (a virus program, an unauthorized download site adding their adware or malware, etc.), and we recommend that you download the software again.
Internally, Authenticode uses the SHA-1 and SHA-256 cryptographic hash functions to confirm file integrity. These are more secure than MD5-based file "checksums".
Windows Store and Windows Phone apps are signed and verified automatically by the respective store mechanisms.