Windows can run every desktop tool in the comparison and it can also run the browser tool without an install. I start in the browser. The file picker is enough for IPS, BPS, and UPS of cartridge size. I install a program when the job is narrower: Lunar IPS 1.03 when I am living in IPS, NUPS 1.4 when I want UPS offsets, Floating IPS when I am writing BPS, Delta Patcher 3.1.6 when the image is a DS card or a disc. Versions and dates are on those guides. 7-Zip or Explorer extracts the zip. Patch the extracted file if the browser did not unpack it.
SmartScreen warnings can reflect an unrecognized app or download reputation; they do not establish that a file is safe or malicious. Read the publisher line. If there is no publisher and the download did not come from the project page named in the tools table, do not run it. A search result called ROM patcher download that is an installer bundle is the thing the safety page is about. This site does not host those executables.
Emulators after a successful patch are ordinary: mGBA for GBA, Snes9x for SNES, a current N64 emulator for .z64, melonDS for DS. The patcher does not configure them. If the game boots to a black screen, go back to the checksum and the header before you change video plugins.
Related pages: the four desktop guides, the safety page, and the Mac page if you are switching machines. The browser remains the default on both.