I once used quite a few stomp boxes ( flanger, phaser, chorus, delay, eq, octave etc.) with my bass, but it really killed the tone/signal from my bass to the Amp, so I switched to rackmount units ( shorter signal path) ....... bass to rack to Amp, now I just use one unit in my Amp's FX Loop, sounds much better, I'm not a big FX person but some of the stuff I play requires it, or I add it for a solo ( chorus, octave, delay) and some times I use 3 pedals Crybaby Wa Wa 105Q, Bass Whammy, and Blue Tube, some pro players use all rack stuff, some pedals ( Doug Wimbish) and some have both incorporated with one of those Bradshaw like custom rack systems ( Chris Squire) Its really personal preference and what type of things you play.
I currently use a ART SGX Nitro with 2 of my setups and a Lexicon MPX G2 in the other, the ART is very user friendly and the MPX is a little more difficult , but it can do some insane things, I also have an ART Nightbass that I put my Chapman Stick through for the preamp with some reverb.
I agree with AJ's comment about using FX like a condiment. but in the end there are so many choices.............