Rootbound Defenses is a good instant-speed answer to board wipes, even if you don't use the populate mechanic. Deathless angel and Avacyn can grant indestructible. Mother of Runes is also a good option for protection. There are other single-target options like totem auras, the cards Indestructibility and Gift of Immortality. Darksteel plate, Swiftoot boots, whispersilk cloak and lightning greaves are all staples of the format to provide removal protection. Spectra Ward is also decent.