Idea: Colored custom highlights plus highlight tracker
Why not allow people to define colors for their custom highlights? i.e. different words highlighting different colors.
And have some sort of highlight indicator in the status bar that lights up that color when highlighted, then you click it to go to the buffer that the last highlight occurred in. Possibly also make it show multiple highlights side by side, rather than a new color replacing the last unchecked highlight.
[See also http://bugs.quassel-irc.org/view.php?id=263]