It really comes down to preserving the tone identity of what each pedal can do. Having a not well thought arrangement can choke the life out of your pedals. Here is a guide that seems to be followed commonly by guitar pedal board designers and guitar players:

1. Tuners. Seems logical to place the tuner in the first place in your FX chain since you want unprocessed signal to go in it for correct reading.

2. Filters. It would make sense to add these (envelope filters, auto wah, wah pedals, etc.) at this spot. Any dynamically controlled filters are triggered by the signal attack so it would make logical sense to add them as early as possible in the chain so they aren’t limited by other effects.

3. Compressors. Notorious for noise level increase, compressors should also go as early as possible in the signal paths.

4. Overdrive. Since the overdrive pedals are generating overtones (harmonics), they should be placed here. Don’t feed overdrive pedals with modulated signals since they can easily clash with the harmonics. Unless you are in for some really wacky tone.

5. Modulation. It is time to add your flangers, phasers, choruses and tremolo pedals here. They breathe the best here in relationship with the overdrives/distortion pedals ahead of them.

6. Volume. Again, the logical place for a volume pedal, since it won’t alter the signal level entering the overdrive pedals maintaining this way the fully affected tone. Also will let the delay finish its job (delay-ing) when the volume pedal is minimized.

7. Reverbs & Delays. They are the last pedals in the chain since they are hard to tame if placed before overdrives – they can produce spikes in the effect level and upset the overdrives.

Following this pedal ordering you can get a decent tone out of your guitar pedal board.