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Campfire has extremely good searchable chat logs, which are a single click away from any chat room. It has good authorization controls on chat rooms and access to transcripts. It associates uploaded files to transcripts, and has very good UI for finding files across transcripts. Finally, it has a solid HTTP API, which we've used to put chatbots for commits and such on channels. I recommend it.

Downloadable, searchable daily chat logs. It also allows you to upload attachments and lists those next to the daily chat logs. Navigating the raw text logs isn't that great, but it keeps them forever.

I find the search really useful to pull out tidbits of information we discuss, phone numbers, ideas, command lines, etc.

I'm still on the free plan.

IRC with a perm connected client/bot doing the logging? and a nice web front-end (http://qwebirc.org/)