I wrote a while ago about time-based event modeling as an analysis technique. Basically, identify what the system is doing over time explicitly - draw it out - and the patterns you see will point you toward the problem (or problems). This is great, but getting a tool to do the actual timeline with is somewhat problematic.
So, what are your choices?
This is a good tool for fairly well-known timelines. However, when you run out of room you can find yourself rewriting a lot. It also is difficult to share this with people who aren't physically present.
Sticky Notes on a Whiteboard
This is my preferred method when remote access to it is not a concern. You put your events on sticky notes, so that when things get crowded or your understanding changes you can simply move them around. This does have a problem that you better use good sticky notes; you don't want to walk in one morning and discover that the stickiness has worn out and your timeline is now on the floor.
This can be done on paper, in Excel, on a wiki, etc.; the format choices are numerous. This one has the advantage of being shareable. However, I find it makes it a lot harder to see patterns. Lists can't show gaps, or different rows for different components.
Online Timeline Tools
In general, these tend to be a bit finicky. They show timelines with icons, colors, gaps where nothing happens, etc. However, they're often hard to use. We have just started working with the SIMILE timeline, though, and it's working great. Once it's set up, adding elements and moving them around is very simple. The integration with graphs and charts is very nice, as well. My thanks go to Michael Fortson for pointing out this one. When remote access to the timeline is important, definitely check this one out.
In the end, the tool you use is up to you - go for the sticky notes or the list or GUI timeline tool. Just make sure your tool helps your analysis and doesn't stand in the way of seeing the system patterns.