I think that there are about 13 or 14 landmarks including the ones in Alien Crossfire. There is one landmark that I know of that has factionwide effects, and that is the Manifold Nexus (SMAC/x). If you have this landmark within your borders, your faction gains a +1 Planet, if I'm not mistaken. As for which ones are best to have in your territory, I think it depends on your playing style. Since I am an energy fiend, I make sure that I have Mount Planet, Pholus Ridge, Uranium Flats, Sunny Mesa, The Borehole Cluster, and the Geothermal Shallows within my territory. I also like having the Monsoon Jungle in my territory, as it boosts food production. If you like good mineral production, go for Garland Crater or Mount Planet. For nutrients, get the Monsoon Jungle, or the Freshwater Sea.
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"Shake the world beneath your feet up"
--Johnny Clegg