Quick thanks to Ochita2001 for starting this topic, and Meowfullz for the Probe Guide! I'm just gonna post some map pictures here for folks who are still having trouble finding the probes. I'll toss in the clue locations too, but they don't do anything yet and I'll likely be changing their locations so don't get too attached to them!
I would post pictures for each probe on its own, but I'm lazy and don't want to play through the game taking screen shots for each individual probe (and clue) so I hope the maps aren't too hard to read.
Farmstead:
Metropolis: (Don't forget that you need to find the evil sewer creature to get a key to the Evil Residence, where three of the six probes in this level are hiding!!)
Sewers:
Area 51:
The last four Probes in Area 51 are on a table in the next room, they're not really hidden at all.
Hope this helps!