The secret tones I mostly had a hard time with (There are exceptions), weren't the one's derived mainly from a more traditional pedals approach. It was the rack rig tones, that were always elusive w/ a pedal approach as a solution, for me.
There came a point that I realized the core tones were from certain guitar/amp/speaker/cab combinations. Then if a TS9 was utilized as a part of the tone 'Core'-- then that made a difference too (obviously).
I figure the core amp tones seem to revolve around Fender, Mesa, Marshall, Vox, Hiwatt, and Roland (JC-120). Most current amps are a modded/blended version of these.
Then came the 80's-- MIDI gear in guitar rigs, channel switching amps etc...
For me, I like to cover a lot of sonic territory, because I play a few different styles of music, and since I play live and in the studio too, I needed to consider real time switching, as a prerequisite for my rig's design philosophy.
I ended up deciding on a W/D/W, Multi-Amp-- design approach incorporating pedals, along with digital and analog rack gear. The rig can run mono, w/d, w/d/w, wd/d/wd, d/d/d, or stereo. The outboard processing choices came from years of researching what studio tools were used by the engineers and artists whom I admired. I realized that MANY of them were the same devices, so I started there (TC Electronic, Lexicon, Eventide, Dytronics, Custom Audio Electronics). MOST don't go this route, and I understand why-- but when it comes to being able to create, or recapture "secret sounds"-- Let me tell you-- If a variety of options is what you're into-- then there are a bunch of valid ways to approach things, none of which are a substitute for developing skills on one's instrument.