I would like to record my large CD collection into the best digital format -- Ogg Vorbis?

Of the lossy formats that are of higher quality than AAC, Ogg-vorbis is the most popular. I think it is your best bet in terms of sound quality and hardware support. It's open-source and its latest release was on Feb. 3, 2010, so it's still an active project.

If you're using lower bitrates, a possible alternative is Musepack, which is probably slightly better than AAC. But if you're worried about obscurity, this probably isn't the best choice.

High-bitrate alternatives are DTS, AC3, and LossyWAV. Of these, I think LossyWAV would be your best option. You feed it an uncompressed WAV file, and it generates a file with bits removed. You then convert it to one of the currently supported containers (Flac being one of them). The result would be a lossy Flac file (hence a Flac file of smaller size and in the bitrate of your choice). If I remember correctly, the file would have the same playback support as a regular Flac file.

(But I still think Ogg is your best candidate. I mention lossywav in case for whatever reason you don't want ogg.)

Side note-- Monkey's Audio (Ape) isn't a lossy format, it's lossless. So even if you were the only person in the world using the format, you could always convert to another lossless format without any loss of quality. (Unlike when transcoding between lossy formats.)