Chorus/Phaser/Flanger

Generally, you get the expected swooshing sound behind your distortion phase, but placing it beforehand can give a very difficult to describe but interesting sound. I kind of like it in this position, because it has less of a swooshing sound to it, which I find detracts from the actual music. It also makes your distortion character change, which makes it a bit more interesting, especially if you're playing a very repetitive part, such as straight palm-muted single notes. I use mod effects in both positions.

EQ

As mentioned in the amp/tone page, EQ before distortion has a much larger effect on how the distortion operates than how the frequency response is changed. I generally use a single Studio EQ or Mid-Focus EQ to sculpt the distortion character, while I use multiple Parametric EQ's and/or a Mid-Focus EQ after distortion to dial in the desired frequency response in my final tone.

Delay/Reverb

I don't know how anyone gets away with putting delay before a distortion phase. The distortion will compress it and cause the delayed signal to be just as loud or nearly as loud as what you are currently playing, sounding like two guitars fighting for space, playing different things at the same time. People have said EVH put his delay in front his amp distortion, but I can't get it to sound right. I think they're wrong and his echoplex was being used for tonal changes, not actual delay.

I generally put my delay and reverb last (or close to last) in the chain. I don't think it matters which goes first. Occasionally I'll use two delays.

Pitch Shifters

(Octave, Whammy [Pitch Glide], Smart Harmony) - I like these in front my distortion phase usually. The whammy especially sounds more like a real whammy bar that way. Smart Harmony I like behind my distortion - then it sounds like you're playing with another guitarist or double-tracking it. When in front, it sounds more like you're playing double-stops. Experiment with the mix when pitch shifting, especially when you put it in front your distortion - low settings will subtly change your tone rather than sounding like you're adding another track at a lower volume.

Sorry if this section is a little light, but I'm not so much an effects guy. I focus on getting a good distortion sound, rather than layering up a bunch of effects.

Top of Pod Setup

M. Gain Staging

I. Principles

You've probably heard the term before but don't know exactly what it means. A gain stage consists of an attenuator and an amplifier. The attenuator is usually attached to a knob or dial. This lets you attenuate the signal appropriately to get the desired tone from the amplifier. Depending on the type of gain stage, you may want to allow the amplifier to distort or to remain clean. Gain staging simply refers to how to set multiple sequential gain stages to achieve the desired tone while minimizing both noise and unwanted distortion.

Analog signals have a certain noise floor that you cannot shrink by attenuating the signal. Thus, the lower volume your signal is, the lower the ratio of the signal to your noise floor. If a low SNR signal is amplified, all that noise is amplified as well. If one gain stage introduces noise early in the signal, you will not be able to remove it later on. To get the cleanest, least-noisy tone, you want to set all your gain stages as high as possible. You use the last gain stage to control final volume - it has the least potential to introduce noise into the tone.

On the other hand, when an amplifier tries to boost a signal beyond its physical capacity, the signal gets distorted. Some gain stages are designed to distort in a pleasing way while others are not. Assuming you want a perfectly clean signal, you must attenuate the signal enough at each gain stage enough to prevents its amplifier from distorting.

Thus, gain staging is often about finding the sweet spot for each gain stage to minimize both noise and distortion. Most of the time, your signal chain isn't very complex, and gain staging is simple. Other times, when you are running unconventional chains and lots of effects units, it is essential to tweak just about everything.

Making things more difficult, some pieces of gear do not feature a complete gain stage, offering no means to attenuate the signal as it inputs the unit. On a hot signal, it may clip in an undesirable way. Your only options are to attenuate the signal via an additional piece of hardware before that unit or to reduce the output of the closest prior gain stage.

If you want distortion, you're probably not going to get the distortion you want by diming every gain stage in your chain. I find it's best to start by setting everything low enough so that there is no distortion anywhere in the chain. As you start to turn up any particular gain stage, make sure that others aren't being pushed into distortion as well - as you turn up one, turn down the next one in the chain. You want to determine which stages produce musical distortion and which should be kept clean. Once you identify the musical ones, you want to find appropriate proportions of one to another.

For example, when running a distortion pedal in front of an amp, sometimes you want to use mostly the distortion pedal's distortion, letting the amp stay clean or relatively clean. Other times you want the distortion pedal to provide a touch of distortion but let the amp provide the bulk of the distortion. Sometimes you want an even mix - I find this is often true when mixing pre-amp and power amp distortions. The main thing to remember is to avoid clipping other pieces of the chain that do not distort nicely. A thick amp distortion may mask that such is even there, but it will make your tone rougher and less defined.