Personally, if you are looking for an open source J2EE app server, I'd tend to go with JBoss if only because it has a much larger market share, making it a lot more likely that you are going to be able to find people that can answer questions or that have done some particular task and have posted instructions.
For the most part, if you are writing a pure J2EE application, it is relatively transparent to the developer what application server you deploy to. If you decide to take advantage of application-server specific extensions, then the choice of app server may matter to developers, but most Java shops are using a rather vanilla setup that can move reasonably easily between application servers. If you want to embrace one particular application server's extensions, there may be some performance/ productivity gains available in exchange for a loss of productivity.
The people that are more likely to care about what application server you are using are the admins. Different application servers have very different administrative interfaces (and different levels of administrative complexity and configurability). The bigger the site and the more critical the application, the more this sort of thing comes in to play. Different application servers also have different JVM implementations which has different performance characteristics. You also have the cost of support. Even if you use a free application server like JBoss, you probably want to purchase a support contract if you are deploying a mission critical application there. If you're deploying something smaller scale where you're comfortable relying on free sources of assistance (i.e. Google, Stackoverflow, etc.) one of the open source app servers is probably a no-brainer.