I've been accomplishing this "transtagging" using the Tag utility found at
http://www.saunalahti.fi/~cse/html/tag.html. I can point this command at any directory of FLAC files and create an identical directory structure with ogg files. I borrowed the first part from Speek's idea earlier in this post.
FOR /R "E:\PATH\TO\FLAC" %i IN (*.flac) DO flac.exe -d -c "%i" | oggenc.exe -q 0 - -o "D:%~pi%~ni.ogg" && Tag.exe --fromfile "%i" "D:%~pi%~ni.ogg"
I can already see that this works well for me because I keep all my FLAC files on a separate drive. If I wanted to put my ogg files on the same drive as my FLAC files, I'd get them all mixed together. I don't know too much about the windows command line, but I'm sure you could just add a little to the "D:%~pi%~ni.ogg" to get the oggs by themselves.