Tony's analysis is accurate, but I'd value his conclusions slightly differently.
I've got 3k oggs on one player and 15k on another (and constantly uploading more files to both), and was running v3a7 for over a year until just recently when I upgraded both to v3a8. I either listen to a specific album or a down-down-down shuffle, so I'm not doing any advanced playlist management. I encode at -q 6, nominally 192 Kbps.
There have been no real problems with the "unstable alpha version of the player software". All of my major issues seem to have come from the different ways that emplode and jemplode manage the files. I had a real problem that came from a file deletion action that created a hole in the fid numbering that never got filled in. There are a number of minor issues related to the alphaness of the software, like songs being marked and such, which may be too annoying for some people, but hasn't bothered me. YMMV.
There are enough tools to organize, tag, and edit ogg files.
foobar2000 does almost everything anyway, and is as high quality software engineering as the stuff from our beloved Empeg Towers. The tools are different than what you might be using for mp3 files, true, but there's enough of them out there.
Ogg files don't work on very many players =compared to mp3= but there are a lot more
ogg compatible players than you think. Additionally, if you're encoding your mp3's at 256+ Kbps you're not going to get many onto most hardware players anyway.
(Vorbis has support for bitrate peeling where you can on-the-fly make a copy of the file at a lower bitrate, but nobody's built a real tool for it yet. Theoretical advantage.)
At 128 Kbps ogg vorbis is significantly better than mp3, but at higher bitrates both files quickly reach transparency, and the difference in size at that point is much less significant. There are very few people who can honestly (in a double-blind test) tell the difference between either at 256 Kbps and the original source material. There are many who claim to, but don't use a valid test methodology.
Mp3 maxes out at 320 Kbps, ogg vorbis can go higher. Some hardware players can only decode ogg vorbis up to a certain bitrate.
Ogg vorbis is more computationally expensive, but there have been a number of improvements in the tremor implementation and such over the last few years so that this factor has improved. In any case, a mk2a has memory and cpu to handle this.
Ogg vorbis is natively gapless, if that matters to you.
Ogg vorbis is open source/patent-free unlike mp3, =if that matters to you.= (Yes LAME is open source, but that's just one encoder not the standard itself. Someone somewhere is paying royalties on mp3 technology even if it isn't you.)
The tag capabilities and standards of ogg is =so much better= than mp3, though this probably is not be an issue to most people, but it is true.
Ogg vorbis files are harder to share because your friends probably can't listen to them, and certainly not on an iPod. (Transcoding is bad even though we all do it at times.)
So there is no objective best. Both have quirks and frustrations that may or may not matter to you.
I think I stayed pretty objective about all that, at least I tried to.

--Nathan