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Tone
,→True vs. Buffered Bypass
Amplifiers are typically high impedance devices, capable of accepting both high and low impedance signals without any change in tone - they don't care if you are using buffered or true bypass. If you notice a difference in tone when running through your pedal in bypass mode vs. plugging directly into the amp, the change is likely due to your cables or the design of the bypass circuit (or a weak battery in a buffered bypass pedal).
=== Boosts and Frequency Response ===
Many pedals are designed as ''boosts'' for your amp. They increase the volume of your guitar signal before the amp, forcing the amp into distortion. Most of the time, distortion pedals are used as boosts, by turning the drive/gain all the way down and the output/volume all the way up. A lot of hype surrounds certain boosts, believing the circuit is doing some kind of voodoo that can't be explained in simpler terms or matched by other devices. Its true that analog circuits can get quite complex; however, it does not mean they are beyond comprehension.
I think the most obvious thing about any boost pedal is its effect on the signal's frequency response. It's no secret that the frequency response of the signal fed into a distortion stage heavily influences the nature of the distorted tone that results; it helps explain why certain types of pickups are favored for certain tones. Some of the most revered boost pedals, such as the Ibanez Tube Screamer, use a high-pass filter to reduce the amount of bass in the signal. This tends to tighten or focus the distortion. Most also have a tone knob, which acts like the frequency control of a parametric EQ that is set to boost - again, this offers more manipulation of the signal's frequency response, altering how the amp distorts.
Now, that's an overly simple explanation. While some boosts may be simple parametric EQ's or high-pass filters, most are often more complex. The tone knob may control multiple parts of a circuit, adjusting multiple filters and multiple values on each filter simultaneously. It may use positive or negative feedback, which not only influences frequency response but also alters the signal over time. And there may be some compression or distortion involved, which may affect some frequencies more than others.
=== Dirt, Distortion, and Fuzz ===