It is possible to run multiple instances of Nutch from within the same tomcat container. I saw this reference on the mailing list and I thought I'd bookmark it here for future reference:

GettingNutchRunningWithDebian - Nutch Wiki

The Title of the page says that it's for Debian, and the instructions do have some specific debian components, but the general idea is platform independant.

Along the nutch line of thought, I also ran into this link: WWW2006 - Geographically Focused Collaborative Crawling which has a presentation on geographically focused collaborative crawling - which in and of itself doesn't apply much to my future plans, but some of the content has natural crossover with the thought of using bayesian algorithms to harness a large scale web crawler to a single vertical market.