Noise IMHO is the main bugaboo of pedals, and it will kill your sound.
One thing I'd like to discuss about pedals is powering them, because that can be pretty important, not just in terms of convenience but how the rig sounds, especially if you have an amp that doesn't make a lot of extraneous noise -- for example, the PRS HX/DA I play through is dead quiet even with the gain up until I hit a note. Two-Rocks and some other amps of note are also very quiet in terms of hum and noise.
After many years in the studio, I'm a stickler for eliminating hum and noise, because I am certain that audio signal coming out of a quiet background sounds crisper, more dynamic, and just plain better than signal coming out of a hashy or noisy background.
This means that the noise that often comes from a pedal board can interfere with the integrity of a player's tone.
Unfortunately it's very easy to get hums and buzzes when pedals are wired up, and if you have ground loop city on your pedalboard, even the best cables are going to let you hear all that hum and noise clear as day. And some pedals are susceptible to noise from nearby wall warts, etc., though IMHO the ones that are really well designed are far less likely to react to stray EMI/RFI.
I've done a lot of experimenting, found that the easiest solution to this problem is to use a high quality, fully-isolated, well-shielded power supply, like the ones made by Voodoo Labs (and a few others, but caveat emptor, there are power supplies on the market that simply suck).
It's also important to use the power supply as the designers intended, that is, only one pedal per isolated outlet. In the case of a paired outlet (for example, you often see a pair of 9V and 12V outlets meant to be either/or, but not both), yeah you can sometimes run a pedal into each one, but you then lose the benefit of the isolation, and you get noise, as I will explain below. I have found that even the Boss TU2 and TU3 with the extra outlet will cause noise if you create a daisy-chain using other pedals, because the extra outlet is not isolated. Yeah, it's convenient as an emergency thing, but not the way to go if you have a lot of stuff on your board.
As an experiment over the weekend, I tried a variety of pedals using the extra Boss TU3 power outlet, and using the extra outlet of a paired set of outlets on my Voodoo Labs power supply, just to see what would happen. In both cases I was careful to make sure that the power draw of the attached pedals did not exceed the available power.
And in all cases, my board went from absolutely dead quiet, to the creation of a very low-level, almost imperceptible hum that I could hear from my amp. Even though the hum wasn't bad, it was audible, and it's that kind of thing that screws with your tone. Worse, when I tried a digital pedal with a tap tempo, and later tried a very well designed analog tremolo pedal, I could hear a slight ticking.
When I reconnected the pedals as the unit was designed, the hum and the ticking went away. Period. No noise whatsoever.
I'm convinced that the smart thing to do if you run out of power outlets for your power supply is simply to buy a second power supply and use that instead of trying to create daisy chains, etc., because these days you can buy a small power supply with 5-6 outlets for around $100, such as the Voodoo Labs iso5, and it really does a better job than trying to create daisy chains of various kinds.
The next issue with some pedals is that certain pedals are not well shielded, and are VERY susceptible to picking up noise from nearby wall warts, or power supplies that are poorly shielded. And this problem is made worse if there are any ground loops, etc, because ground loops tend to act like antennas for noise.
Manufacturers like TC, Fulltone, etc., shield their products properly, and/or use steel casings that tend to reject RFI/EMI. A Fulltone wah will not pick up noise like some of the other wahs out there (by the way, I've found that the typical cast wah casings don't work as well as steel ones), and I'm sure this is the case with any of the good manufacturers -- but I've had wahs and other pedals by builders that go absolutely bonkers if a wall wart is within 5 feet of the pedal board. So that's something to check for. If you have noise, the first thing to try is move the darn wall warts farther away (and frankly, if I had a pedal that reacted to wall warts badly, I'd get rid of it, but that's just me)!
Anyway, hope this info helps, as it does make a difference!