This is the first band I thought of as well. I still remember the article from when Melloncollie was released... at one point in "Through the Eyes of Ruby" they have 50+ simultaneous tracks going on at once. But then again, thats the Smashing Pumpkins + Flood and not us
Jimmy's pretty much spot on. The Pumpkins had a lot of things going for them on Cherub Rock.
1.) not all 40 layers are playing at the same time. One of the first "wow, that's cool!" moments that got me started thinking about arrangements, before I even got interested in chorus, was that single (ok, it's probably at least doubled) clean-ish guitar, possibly accompanied by an acoustic, playing a single D chord mixed way back behind that huge D power chord that opens the chorus, and then just sustains there until it fades out. It's subtle, it's easy to mix, but it adds a nice amount of space to it. Likewise, there's that clean introduction (grabs iPod) which sounds like two VERY tight tracks that start centered and then split, and either way drop out after the distorted guitars come in, and then there's a couple tracks of low E/octave riffing going on (maybe 4...?) while above that there's that ascending octave guitar playing a different part. You hit the chorus, and another batch of guitars, EQ'd to fit into a different part of the sound spectrum, comes in, playing what sound to me like the same chords in a different register and possibly a different inversion. And then, coming out of the chorus, there's a lead guitar doubling Corgan's "uh... huh." vocal, and of course another radically different sounding "lead" guitar, which is either phased or doubled (maybe the later, since that "guitar blowing up" sound is probably tough to double-track, but I'm not sure), and then the lead fills with yet another guitar sound after the solo when the bridge comes in. I mean, there may be 40 guitars in total going on in this song, but they're not all playing at once, and they're not all playing the same riff and the same chords. It's like a jigsaw puzzle.
2.) Corgan's voice. Even as a fan I have to admit calling him a "singer" is sometimes slightly charitable, but there's no question that he's singing "over" the guitars in pitch, and that a guy with a lower pitched voice would be fighting against the guitar sound.
3.) the guitar tone itself. The Pumpkins are fairly gain-y for such an orchestral band, but their "wall of sound" guitar approach is actually a fairly narrow tone (or rather a collection of a whole bunch of fairly narrow tones). No individual guitar tone is terribly expansive.
4.) See #1 - all of the parts are rhythmically very tight (except the wonderfully chaotic lead). Your ability to layer guitars is entirely contingent upon your ability to play the same part perfectly over and over again.