My favorite would have to be either
TWW or
TP Ganondorf. On one hand,
TP Ganondorf was much more evil and powerful, and had some very dark lines, but
TWW Ganondorf had a more sympathetic character and was deeper, like a real person.
The thread needs a poll added.
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The Legend of Zelda games completion status:
Played, but not beat/Simply Beat/100% complete at least one quest/Not played at all (not counting 2nd quests in any category)
LoZ, AoL, ALttP, LADX, OoT, MM, OoS, OoA, TWW, FSA, TMC, TP, PH, ST, OoT3D, FS:AE, SS