I've heard people talk about running certain pedals through the effects loop rather than going from the guitar to the pedal to the amp. What difference does it make and what pedals would you use it for?
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you use it for modulation pedals like flanger phaser ect. you can only run them through a loop if your amp has a loop for them as well. otherwise its just all into the amp through a signal chain.
The Gear:

Custom Strat
Mesa Boogie Stiletto Ace
Fulltone OCD
Electro Harmonix Small Clone Chorus
Dunlop Crybaby Classic
MXR EVH-117 Flanger
Fulltone Soul Bender
Well it all has to do with the order of effects. Just like you have to figure out which order of effects you want in you chain. When you run effects through a loop the effect is added after the pre-amp so most of the tone has already been shaped before it reaches the pedal. So just screw with it for a while and figure out what sounds best where. But to save you some time, time modulating pedals like reverb, delay, flange sound best in the loop.
check out the link in my sig, cuz i recorded the differences between having pedals in and out of the effect loop.
Ovation Celebrity
Ibanez Prestige S1220WNF
modded Ibanez GAX75
Fender tuner-DIGITECH EX-7-BOSS SD1-Ibanez CF7-Tech 21 TM 60
(LOOP)Boss DD20(Loop)
My soundclick page
anything in the loop is after the preamp, and usually it sounds a lot better to delay the final result than to delay it half way through the process.