Is there some sort of problem between the two groups on your campus? What's going on that prompted this question?
Alpha Phi Omega isn't an honor society and doesn't have a national minimum GPA requirement, whereas Sigma Alpha Lambda requires a minimum GPA of 3.0.
Their missions overlap, but the two organizations seem to take generally different approaches. See
http://salhonors.org/membership/statement-of-purpose/ and
http://www.apo.org/aboutus . From my perspective, there's two significant differences. SAL places primary emphasis on academic excellence and academically-oriented service projects in the community, based on that first bullet point. Second, SAL, in their statement of purpose, doesn't take the approach of promoting leadership through service as directly as APO does.
Organizations often have overlapping missions, but they approach those missions in different ways. I think that's a good thing. It gives students a choice. We wouldn't expect men to join a single social fraternity or women to join a single social sorority--we value giving students a chance to find organizations that fit them, to at least some extent (i.e. the fraternity or sorority chooses them as well). Why shouldn't students have the same choices for other organizations? Why can't organizations have similar service initiatives, as long as they benefit the community and nonprofit partners? Should one organization have a monopoly on everything? To me, that would likely hurt the community that these organizations wish to help. There's room on the vast majority of campuses for more than one organization focusing on service and leadership development.
Service is everyone's territory, and there's room for every organization to develop service-related initiatives if they choose to do so.