I've been using wu-ftpd for about 6 years now, and despite a few security blips, it's been quite good to me. I have no major complaints.
However, I find myself using it less frequently than I used to, and after some research, I'm in the process of moving to a different ftpd.
Originally I was considering Proftpd, due to its popularity (it seems to be about #2 after wu-ftpd), but I've never been a big fan of it. I remember when it's backers were constantly talking about how it was so much more secure than wu-ftpd, but then a rash of security issues were discovered, and those claims pretty much died.
After more research, I narrowed it down to lukemftpd (the NetBSD ftp daemon, of Luke Mewburn's work) and vsftpd. I'm almost as much of a fan of NetBSD as I am of Debian, and I've long used lukem's ftp client as my primary ftp client. At the same time, vsftpd is being used by quite a few high profile groups (Red Hat, SuSE, Debian, GNU, Gnome, KDE, kernel.org, sunet.se, sunsite.org.uk, etc), and they do a great job of explaining and detailing the design and implementation behind it.
So, I've settled on vsftpd. I'm setting it up right now, and will post if I have any issues, problems, or other comments on it.