I have played Zelda 1 (NES), LttP (SNES), LA (GB), OoT (N64), MM (N64), OoS (GBC), OoA (GBC), tMC (GBA), TP (Wii) & PH (NDS). Of these, OoT is my favourite of the 3D series and OoS/OoA of the 2D series, with LA just behind. Least favourites of the 3D series was TP, and of the 2D series tMC; both felt paint by numbers to me.
LttP seems to be highly regarded but I always thought the GB/C ones improved upon the formula considerably. They seemed a lot more willing to deviate from the Zelda formula, which might not be surprising considering they would have taken much less development and had lower associated costs.