IIRC, there is a FLAC commandline decoder. Under the assumption that it is called "flacdec" (probably wrong, but you get the point), which decodes a FLAC compressed file to console (not to a file), a usable commandline would be:
flacdec "filename.wav" | oggenc -q 5 -o "output.ogg" -
obviously, you'd need flacdec and oggenc to be in your path (/bin, /usr/bin, c:winnt or whatever your current OS likes)
for doing the same to multiple FLAC files under windows, try the following:
for %f in (*.flac) do flacdec "%f" | oggenc -q 5 -o "%f.ogg" -
the only problem with this command is that you get a bunch of files named .flac.ogg, but that's nothing a short perl-script can't fix.
If the windows commandline supported escaped characters (fat chance that'll ever be impletmented), i'd write:
for %f in (*.flac) do flacdec "%f" | oggenc -q 5 -o "%fbbbbogg" -
but alas, the commandline has gotten worse and worse ever since win98 :
if you are running a pre win2k version of windows, you might need to do a LFNFOR ON in the console first.
feel free to use any other quality parameter, that you like