I've never used this tool so I don't know the commands and this might have errors, but you need quotes around your paths. I also tossed in a /r so it will recursively look through all sub-folders (F:\GC_Games\Smash Bros would be included in the loop for example).
To find more file extensions just add them in the parenthesis part (*.iso *.gcm). This prevents getting other types of files. Using (*.*) would pass all files.
Code:
for /r "F:\GC_Games\" %A in (*.iso) do ("C:\Program Files (x86)\Wiimm\WIT\wit.exe" COPY %A --gcz "%~nA_scrubbed.gcz")
To find more file extensions just add them in the parenthesis part (*.iso *.gcm). This prevents getting other types of files. Using (*.*) would pass all files.