iChat
A couple versions back, Apple updated iChat so that instead of just storing each chat log in a "flat" directory, it organized them by date. Of course, it didn't go through the potentially thousands of chat logs you already had and update their organization accordingly. So that was Problem #1.
Back in the technological dark ages - earlier this century - when I had to go into the office to work, I frequently had multiple computers logged into AIM. The computer I was sitting at during the course of a chat would be the one that logged the two-way conversation, while the one (or more) computers that were logged in but at which I was not sitting, would only get the one-way communication (from the person I was chatting with). I wanted a Single Archive of all My Chats, which requires merging thousands of chat log files (ie, keep the two-ways, dump the one-ways). And that was Problem #2.
Thus I give you a Perl script for organizing iChat log files that sorts out the duplicates. Just run it like this:
mkdir ~/Desktop/Dulicates
perl ~/Downloads/chats.pl ~/Documents/iChats >> ~/Desktop/chats.out
You'll need to update the $DUPLICATES value near the top of the script to properly point to wherever you want duplicate chat logs moved to, and this assumes that the Perl script resides in your Downloads directory. Finally, it creates a log file of all of the actions it performs in the chats.out file on your Desktop.
Use with caution.