There's nothing really special about developing a Trapperkeeper application as compared to any other Clojure application, but there are a couple of things we've found useful:
Since Trapperkeeper is intended to help modularize applications, it also increases the likelihood that you'll end up working with more than one code base/git repo at the same time. When you find yourself in this situation, Leiningen's checkouts feature is very useful.
If you need to test the shutdown behavior of your application, you may find yourself trying to do lein run and then sending a CTRL-C or kill. However, due to the way Leiningen manages JVM processes, this CTRL-C will be handled by the lein process and won't actually make it to Trapperkeeper. If you need to test shutdown functionality, you'll want to use lein trampoline run.
However, one quirk that we've discovered is that it does not appear that lein's checkouts and trampoline features work together; thus, when you run the app via lein trampoline, the classpath will not include the projects in the checkouts directory. Thus, you'll need to do lein install on the checkouts projects to copy their jars into your .m2 directory before running lein trampoline run.