Foobar2000 supports WMA tags in the meantime, meaning you could use it to painlessly transcode your collection to another format of your choice, without losing the metadata. Its converter serves as a GUI for command line encoders, allowing a quick setup and ReplayGain scanning of the resulting data. Tags are automatically transferred between the formats, no need to rely on metaflac.exe, metamp3.exe and consorts.
Lancer is considered being the best available Vorbis encoder. It is based on
aoTuV and incorporates fast SSE optimizations. Depending on the quality of your WMA Pro files, you should consider transcoding to high bitrates in order to maintain an enjoyable listening experience. -q6 (~160 kbit/s) should even suffice for low-bitrate input data, -q4 (~128 kbit/s) could be of interest for very high quality sources. Download the SSE optimized oggenc binary and set it up inside foobar's converter in order to start the job.
Of course,
FLAC would be the best possible solution, causing no further quality loss. At least if file sizes were of no concern.
On
Rarewares you'll find the decent LAME MP3 encoder. I'd recommend going for the latest 3.98 beta with a quality setting of at least -V 2.
Since you consider the patented MP3 as an option, MPEG-4 AAC could be of interest as well. It enjoys decent hardware and software support and has proven being of high quality in the latest listening tests.
Nero's command line encoder works with foobar as well, a suggested setting would be one similar to the average bitrate of the Vorbis recommendation, like -q 0.5. Alternatively, high quality sources might also go with -q 0.4.
This is actually a wide variety of possible formats. The choice which one to use is up to you, since no current listening tests with transcoded material are available on this site, at least none which included representative audiences. There's an old transcoding listening test by Guruboolez somewhere, who summarized that MP3 was the worst possible choice for transcoding jobs. But this was the opinion of a single individual, and the codecs he used aren't up-to-date anymore.