I like to look at it from a production/mix point of view. When you're in the studio, you might use layers of guitars to add or subtract depth and dynamics. Also in the studio your bass would normally be compressed and the level automated (boost for chorus or heavy riff or whatever). I try to replicate my approach in the studio using effects.
So, instead of having to have a 2nd guitarist, I create a "thickening" effect with distortion, some modulation, and some EQ. Instead of hiring a soundman to learn all of our songs, I can use pedals to boost the low end where it's needed in the sounds, and likewise to compress the bass and automate the levels if needed.
On top of all that I love to create weird noises. Some of the music I play is a bit atmospheric, and while a low end drone can be very nice, it gets a bit boring after a while. My whammy and feedback loop help me enter much higher registers. Much like the high C on my 6 string basses, I feel it gives me extra room to play and be melodic in these atmospheric situations.