It seems to me that Shankara and Shamkara both would be fine, although my personal favourite would be Shankara (I believe this is the most usual rendering, too, when indological transliteration isn't used). The forms with -c- are somewhat confusing, since some people might think that the c should be pronounced -tsh-. Zankara is out unless you are using indological translation in the Kyoto-Harvard format. Sankara misses the Indic sound at the beginning of the word. Generally, you cannot make a difference between the three s's unless you use indological transliteration, but you can differentiate between two s's, normal s and sh, which would stand for both z and S in the Kyoto-Harvard format.