I'm gonna shamelessly quote Max Andersen's response to the exact same question on the m2e's mailing list :
m2e(clipse) = the core plugins that enables Maven to read and understand pom.xml files and then configure Eclipse based on these pom files. m2e also has an extension mechanism to allow other plugins to add explicit support for specific maven plugins. m2e is developed at eclipse.org.
m2e-wtp = an extension/plugin for m2e which provides explicit support for Eclipse WTP project and configures WTP based on the maven war, ejb, ear etc. maven plugins found in pom.xml. m2e is developed at jboss.org/tools and made available via the Eclipse Maven marketplace.
So far, it's not settled yet if JBDS 5 will embed m2e / m2e-wtp directly. But even if it's not, an "extras" update site will allow you to install these plugins easily from JBDS 5.