One of the projects I am working on presents a series of events related to a court case. The timeline is perfect to point of gaps in events or relationship between events. I have some canvas code that lets you lasso draw around an area, which I would use to allow someone to draw around a group of events as a way to highlight that series.
Also, there is a view that shows a collection of financial transactions over time. Some transactions are related to each other, but that can be hard to see in the timeline, even with colors. Drawing lines between the related items is a way to show the flow of those related transactions as they happened in time relevant to other financial transactions.
Finally, when there is a gap in an expect event flow, like 1st and 15th (such as missing payments, etc.), then that gap should be highlighted in a way that is not the background colors supported already.