If your playing live it's slightly more complicated, but you can get something like a Radial Loopbone (
Tonebone Bassbone - introduction) or similar to keep your signal clean without pedals on, then turn them on when you want them. Put a volume or EQ pedal in the loops if you need to raise the level to match your straight-through signal.
If your just recording or playing at home, just minimize the number of pedals used at any one time, and most importantly, buy good pedals! There's a lot of crap out there that many people justify using just because it's all they can afford.
I've been collecting vintage pedals for a while now and I really like the way some of them color/suck tone when I'm looking for a particular sound. For example, a Mutron III can do some nice things to your tone as it bleeds through even though it is "off".
I think pedal makers, much like quality micro-brewers, have their own "breath" or after-taste. I've always hated the very literal breath that all Boss pedals have. It's like they put a digital asthmatic in every pedal. There is so much better out there. Look at modern boutique pedals like Keeley, Analogman or tons more that are way better than anything Boss produces.
Best yet, buy some vintage pedals. You'll find that they are a good investment and will make you money years down the road. Plus, they sound great and most boutique makers are trying to reproduce what the vintage pedals sound like in the first place. Buy the real thing if you can afford it. Compared to the price of many boutique things, the original, vintage pedals aren't that much more expensive.
If I want to eliminate all tone suck, I go guitar straight into amp. I use pedals when I want a particular colored sound.