The closest evidence thing I can find to anyone from the SPLC identifying Project Appleseed as a militia is a 2010 New York Times article [1] about Project Appleseed in which the article (not the SPLC) spends some time discussing Appleseed in the context of militia and Tea Party movements, and someone from the SPLC -- not labeling Appleseed a militia -- is quoted referring to the possibility that someone from an extremist group would come to Appleseed and learn to be a sniper in a paragraph about that being a threat to (not from) Appleseed.
I do find lots of links to that article on right-wing, pro-gun blogs pointing to this article referring to it being the NY Times and/or SPLC and/or the Jews supposedly behind either or both of those organizations targetting Appleseed, but I don't see any evidence that the SPLC has actually labelled Appleseed a militia.
[1] http://www.nytimes.com/2010/08/01/magazine/01Appleseed-t.htm...
[2] Particularly, its not on this list of Patriot groups (of which militias are subset): http://www.splcenter.org/get-informed/intelligence-report/br...