There are so many but I think Quake3e has taken over as the most popular vanilla client. IoQuake3 is still used but dev is not as active. I found another really cool client actually while making this called Lillium arena classic - which is a client for the early 1.16 protocol of Quake 3. This is the version that was distributed to sega dreamcast and there is actually still an active community (around 50 servers) that play on this version.

But once you get into mods like cpma, defrag, urban terror - as you probably know a lot of them distribute their own client - and most of those are based on Quake3e or ioQuake3