One question I get a lot when I demo FogBugz is, "how do I enter dependencies?"
FogBugz treats a dependency like any other kind of hyperlink from one case to another. If Case 123 depends on Case 100, go into Case 123, hit Edit, and type "Depends on Case 100." FogBugz sees the phrase "Case 100" and automatically makes it a hyperlink in both directions. There will be a link from case 100 to case 123 and vice-versa.
Evidence-Based Scheduling does not take dependencies into account when calculating ship dates. This is intentional, although it may be a little bit unexpected for project managers who have been using Microsoft Project. Here's why: on software teams, it's almost always the case that the team can keep working even when there's a dependency. Software developers have a great deal of flexibility in the order in which things are done, unlike, say, a construction crew building a house. Because it's so easy to create simple stub functions as placeholders, with software, it's perfectly reasonable to build the roof before the foundation is poured.
In practice, dependencies among software development tasks almost never impact the schedule, and software teams are almost always able to keep working at full-throttle even when something they're waiting for is not ready. Therefore, EBS takes the approach that dependencies should not be considered in estimating ship dates.
This is quite the opposite of the construction industry, where Microsoft Project originated, where the entire work site must grind to a halt if the foundation was not poured. As a result, when you use Microsoft Project for software, you get unrealistically conservative schedules which imply that most of the development team is sitting around waiting for something most of the time, even though in reality that almost never happens, because software developers are adept at reordering their work to keep moving forward.
When the software development phase is a part of a larger project with non-software components, dependencies are important. For example, you might have a project that involves hiring programmers, building a data center, buying servers, writing software, and installing the software on the servers. Here, of course, the dependencies are critical—you really can't build the software until you hire the programmers. In such cases, we recommend using something like Microsoft Project to manage the overall project, although you only have to enter a single row in MS Project to reflect the "writing software" part, and you should use FogBugz and EBS to decide how much time to enter for that task.