Remove string retainers and make sure the strings can glide freely against the nut when using the whammy bar.
Install locking tuners to stay in tune and avoid having to wind strings every time they need to be changed.
Install double-coil pickups in the neck and bridge positions. This will provide higher output and reduce the amount of noise present when increasing gain on an amplifier or through an effect pedal.
Purchasing a custom bridge block can add more sustain and improve the quality of your tone. There are drop-in replacement kits for Strat-style guitars that are easy to install.
Lastly, using a Frankenstein approach of combining different necks and bodies with changes in pickups can provide new sounds with different feels to the instrument, and almost endless variations.