The easiest command line you can do is:
"C:\path\to\flac.exe" "C:\other\path\to\input.wav"
This will use the default compression setting (-5) and produce the file "C:\other\path\to\input.flac"
If you want to set a compression setting (-0 to -8) use:
"C:\path\to\flac.exe" -6 "C:\other\path\to\input.wav"
If you want to specify the output file's name use:
"C:\path\to\flac.exe" -8 "C:\other\path\to\input.wav" -o "C:\another\path\to\output.flac"
If you want to verify the encoded file as you encode use:
"C:\path\to\flac.exe" -4 -V "C:\other\path\to\input.wav" -o "C:\another\path\to\output.flac"
Finallly, I would recommend putting flac.exe in a folder in your PATH, like your windows folder. This means that you can then navigate to the source WAVE's folder and use something like:
flac.exe -4 -V input.wav -o output.flac
i.e.: you don't need to always specify the path to flac.exe. If you are in the source WAVE's folder you don't need to specify the full path to the source file, or destination file if you specify one (using the -o switch).
Edit: Sorry, I forgot about tagging. If you want to set tags when encoding use the format:
-T "TAGNAME=VALUE"
E.g.:
flac.exe -6 -V -T "ARTIST=Pixies" -T "ALBUM=Doolittle" input.wav -o output.flac