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It is possible to specify multiple projects. Here is an example of three projects: a generic website, a projects area, and a day-planner (the day-planner part requires Planner Mode—see http://wjsullivan.net/PlannerMode.html to get it).
(setq muse-project-alist
'(("Website" ("~/Pages" :default "index")
(:base "html" :path "~/public_html"))
(("Projects" ("~/Projects" :default "index")
(:base "xhtml"
:path "~/public_html/projects"
:exclude "/TopSecret")
(:base "pdf"
:path "~/public_html/projects/pdf"
:exclude "/TopSecret")))
("Plans" ("~/Plans"
:default "TaskPool"
:major-mode planner-mode
:visit-link planner-visit-link)
(:base "planner-xhtml"
:path "~/public_html/plans"))))
The :major-mode attribute specifies which major to use when visiting files in this directory.
The :visit-link attribute specifies the function to call when visiting links.
The :exclude attribute has a regexp that matches files to never publish.