I personally use Cygwin, which puts the entire smörgåsbord of Linux utilities at my fingertip --- there's md5sum and all the cryptographic digests supported by OpenSSL. Alternatively, you can also use a Windows distribution of OpenSSL (the "light" version is only a 1 MB installer).
Any MD5 will produce a good checksum to verify the file. Any of the files listed at the bottom of this page will work fine. http://en.wikipedia.org/wiki/Md5sum
On MySQL.com, MD5s are listed alongside each file that you can download. For instance, MySQL "Windows Essentials" 5.1 is 528c89c37b3a6f0bd34480000a56c372.
You can download md5 (md5.exe), a command line tool that will calculate the MD5 of any file that you have locally. MD5 is just like any other cryptographic hash function, which means that a given array of bytes will always produce the same hash. That means if your downloaded MySQL zip file (or whatever) has the same MD5 as they post on their site, you have the exact same file.
Note that the above solutions will not tell you if your installation is correct only if your install.exe is correct (you can trust it to produce a correct install.)
You would need MD5 sums for each file/folder to test if the installed code has been messed with after the install completed.
WinMerg is useful to compare two installs (on two different machines perhaps) to see if one has been changed or why one is broken.
When I worked with Windows, I found handy HashTab 3rd party tool. It shows MD5, SHA-1 check sums in one of file properties tabs. http://implbits.com/products/hashtab/
This has worked great for me on windows for a while now. It allows easy copying and pasting of checksums. It has box to type/paste check sums from webpages and show matches or non matches quite well.
for sure the certutil is the best approach but there's a chance to hit windows xp/2003 machine without certutil command.There makecab command can be used which has its own hash algorithm - here the fileinf.bat which will output some info about the file including the checksum.
7-Zip can be used to generate hashes for files, folders of files, and trees of folders of files. 7-Zip is small footprint and a very useful compression utility. http://7-zip.org/