This is a brief evaluation of eight web mailing list archivers: Hypermail, ezmlm-www, Gmane Loom, Lurker, MHonArc, mlmmj, msgcab, and Pipermail. Each has a picture of what the output looks like, links to sample pages, and notes.
Keeping in mind that for many of these programs I don't know their dependencies and how easy they are to install and modify, these are my recommendations:
(http://www.hypermail-project.org/ is slightly more recent.)
What we used now. No release since 2003. Formatting options are insufficient.

Thread view: http://www.hypermail.org/mail-archive/2003/Aug/
Sample message: http://www.hypermail.org/mail-archive/2003/Aug/0001.html
Seclists Thread view: http://seclists.org/nmap-dev/2009/q3/index.html
Seclists Individual mid-thread message: http://seclists.org/nmap-dev/2009/q3/0069.html

Output looks nice. Seems to require an ezmlm installation. [This one doesn't impress me much. Doesn't seem to have a good way to view thread nesting or to indicate where we are in a thread in the individual messages. -Fyodor]
Thread view: http://listarchive.consultech.net/ZossPens/index.cgi?0:200604
Sample message: http://listarchive.consultech.net/ZossPens/index.cgi?0::8784

The web interface used by Gmane. Uses "non-standard, frightening and insecure features in web browsers to try to make it almost pleasant to read a newsgroup with a web browser." May have a dependency on the Weaver daemon. Already does RSS with excerpts. Not quite as easy to link to an individual message, though each page seems to have a permalink or "direct link" option for this purpose. Some of the keyboard shortcuts are really nice. The thread frame on top is a nice way to track where you are in the archive, but I'm not sure if it would work with the seclists chrome. Plus the extra frame can be a bit annoying.
Thread view: http://news.gmane.org/gmane.comp.security.nmap.devel
Blog view: http://blog.gmane.org/gmane.comp.security.nmap.devel
Sample message: http://article.gmane.org/gmane.comp.security.nmap.devel/11807

Said to be highly scalable. Has an idiosyncratic thread view that I don't really like. Latest release was in March 2006.
Thread view: http://archives.free.net.ph/list/dundi.en.html
Sample message: http://archives.free.net.ph/message/20090829.175340.650ee1e6.en.html

Sees use by other projects. Output looks nice and is presumably customizable. Last release in 2006 and no development since then. Has RSS output, without excerpts. Has the highest Pagerank if you exclide list.org, which is more about Mailman than pipermail specifically.
Thread view: http://www.mhonarc.org/archive/html/procmail/2009-09/threads.html
Sample message: http://www.mhonarc.org/archive/html/procmail/2009-09/msg00038.html

A complete mailing list manager that includes an archiver. Output and URL formats is a lot like Hypermail. Lacks previous/next period links.
Thread view: http://mlmmj.org/archive/mlmmj/200907bydate.html
Sample message: http://mlmmj.org/archive/mlmmj/2009-07/1542.html

Looks nice and lightweight, but doesn't look to be maintained and the demonstration site is down.

Strangely enough, it's hard to find information on just Pipermail on the web. I think that it's built into Mailman. Output is plain. Similar to Hypermail.
Thread view: http://mail.python.org/pipermail/python-dev/2009-September/thread.html
Sample message: http://mail.python.org/pipermail/python-dev/2009-September/091513.html
For excerpts we could use t-prot, which cuts out quoted text and long signatures. A howto is at http://freshmeat.net/articles/t-prot.
Gmail is a widely-liked interface for reading emails. We can look to that for some inspiration (e.g. for making look and feel decisions, as they've likely done research and used good designers).