I switched from Logorrhea to ChatMaster because CM can delete unwanted chat files. Its searching is a bit more finicky than Logorrhea's, tho'.

In a similar way that iTunes and iPhoto interfaces can hide the underlying file/folder structure of their data storage I'm fine with iChat hiding its unhierarchical archive folder as long as there's a reasonable way for "virtually" managing/organizing that data. So far ChatMaster's basic interface has worked well enough that I'm satisfied never having to deal with the iChat folder directly from Finder or a Terminal shell.

Moving beyond any default location/structure for storing iChat transcripts I can imagine Spotlight technology in iChat and/or its supporting apps being able to find transcripts (given enough metadata) if users choose to reorganize them differently. In general, that seems a more flexible strategy for certain kinds of applications than if they're imposing specific file/folder structures that users are restricted to using. For example, I hope iTunes and iPhoto become capable of powerfully managing most any user-defined layout of audio and image files, satisfying the requests of folks who want to keep that data organized the way they want it.