Your connection pooling, and efficient use of connections is an absolutely critical part of your entire architecture. Working with WebSphere, I always prefer to defer to WebSphere connection pooling. Why? Bias perhaps, but I like the idea of offloading this important work to the server provider. I'm assuming the server vendor has put more work into making their pooling services more reliable and robust than the ones that are managed and maintained within a give web app or ejb app. Plus, if something goes wrong, I've got the vendor's 'throat to choke.' If something goes wrong with Hibernate connection pooling, whose throat do you go for? With IBM, there's always a sales guy with a sore neck willing to offer support.
Actually, I've always found that JBoss had the best paid support out there, but that's another story.
Beyond just trusting the vendor, I'm not sure of any definitive benefits. Maybe someone else can pipe in? Even my justification is more based on "Fear, Uncertainty and Doubt" as opposed to any real or calculated metrics or comparisons.