This thread would until recently have been very interesting. However, the official timeline has just been revealed, so the time of timeline theories has (unfortunately) come to an end.
Anyway, here is the timeline from "Hyrule Historia":
--------------------/---TWW/PH---ST (Adult Timeline)
SS---TMC/FS---OoT---AlttP/OoX/LA---LoZ/AoL (Downfall Timeline)
--------------------\MM---TP/FSA (Child Timeline)
Note: It is not clear if TMC and FS share the same Link.
The AT and the CT are the ones from the old split timeline. The "Downfall Timeline" (there are other names, though) seems to be a "what if"-story that takes place if Ganonodorf defeats Link in the future (in OoT), although the exact nature of this new timeline is yet not clear.
/Blue Window
EDIT: Vanitas and JuiceJ posted while I was writing.