these applications are separate projects in eclipse. I'm worried that if
I combine them into a maven-ized single project with modules, I will no
longer be able to deploy them as individual web applications within
eclipse (using eclipse web tools project web server - tomcat in this
instance).

AFAIK eclipse WTP expects only a single web app within a project - has
anyone encountered this scenario before, and if so, have they found a
feasible solution that allows eclipse WTP and maven (with multiple web
apps as modules) to coexist?

There isn't a problem using Eclipse 3.1, I use it.
It's slightly annoying, but you just have to check out at the module
directory rather than the project root directory.

With Eclipse 3.2 you can have projects that reside within another
projects directory space.
I believe they are called hierarchical projects.
See http://www.nabble.com/forum/ViewPost.jtp?post=5849132&framed=y

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