I've gotten away from using a ton of effects because to my ears you can definitly hear how they can and will suck the hell outta the true tone of any nice guitar especially in conjunction with a nice amp. unless you really make a sincere attempt to make sure every effect you use is true-by-pass a decision is made on whether you want to sacrifice tone for a nice effect...
not sure why i needed to say that, but anyways i use:
Guitar chain (guitar -> amp):
mxr phase 90 (w/ infamous capacitor mod)
EH Bigmuff (w/ a switchable capacitor mod of my creation to alternate from the original sound to the new increase volume/bass)
EH Deluxe Memory Man
occassionally Mxr/Dunlop Hendrix Octave Fuzz (though i find it too annoying to make it worthwhile in my chain)
amp is an early 70's silverfaced Fender Twin Reverb Hotrodded where the Vibrato preamp tubes are bypassed to give more gain boost... it probably pushes 100W tube power and rivals alot of other larger powered amps, the only bad thing is that its way heavy and abit akward.
I often create/use other sounds in conjunction to playing guitar and i will use these effects:
Korg Kaoss Pad Version I (mostly for Ring Mod mode)
Boss Dr. Sample Version I (w/ stored samples and pitch, ring mod, reverse, delay effects)
mxr blue box (capacitor modded w/ switch to alternate from original sound to new, this used to be in my effects chain until i realized this mod totally altered w/ the sustain ability of my guitar tone in a negative way, it sucked all the sustain, probably there is something else inherently wrong w/ my copy).