Logic analyzers connected to pins on a CPU. You don't see that much any more. The connections they're looking at are inside the chip today. Of course, now we often have JTAG access to the innards.
Let me emphasize that there's no CPU chip in the Alto - the CPU is made up of dozens of TTL chips on three different boards. We're tracing the individual microcode instructions that the Alto is running. As Animats points out, this would be deep inside a modern chip.
There's a brilliant talk, given in 2009 at HOPE09, NYC titled "Indistinguishable From Magic: Manufacturing Modern Computer Chips".
At roughly 36 minutes, there's a cross-section of a (in 2009) modern chip. The topmost layer is the shiny rainbowy topmost metal-layer you see on typical (from the top) die photographs. The very, very small comb-looking bottommost-layer is the individual transistors, and structures there are of the size that give a "xxx nm" process its name.
I very much recommend everyone to watch this video, to get a sense for the complexity that goes into producing a modern CPU.
To come back to the thread I'm answering here: The logic analyzer on the Alto (probing microcode) connected to interconnects of individual gates probably would be connected to signals somewhere in the lower middle of the stack in a modern CPU, I guess.
