Back in the days when I used Trillian there was this nifty and very useful feature that I miss almost daily in Colloquy:
Trillian displays an horizontal line in the transcript window at the moment in time when it lost focus (or when you moved to another channel). That way, when you come back to that channel or when the app gained focus again, you can easily read back. The black line tells you exactly what the last line was that you saw/read in the transcript. While you are away from the app, the new messages are displayed below this black horizontal line.