Actually, I noticed it's only the Leonardo that has two caps. The Uno does not. Nor does the Ethernet.
Futhermore, the Leonardo's two caps are connected on the 5V side of the diode and resistor, then to ground. But the single cap on the Uno and Ethernet is connected to the reset line and ground.
The two are very different circuits, and neither one seems to work as it's supposed to with the simulator I'm using. Instead of the results I was getting before which mostly made sense, now when I flip flop the DTR line, I just get 5V or 0V on the reset line, and the voltage doesn't revert via the cap as before:
I also see no action on the diode. It seems to do nothing.
Is the simulator broken? It could be. But if it is, what about the different placement of the caps in the schematics? Which is correct? Do both work, or is one wrong?
[edit]
I guess the main difference is in the Leonardo you have two caps to ground, with a resistor between them and the reset line, whereas in the Uno you have one cap to ground with no resistor between it and the reset line. So I guess they're not totally different. But still no clue which is better or why they're different.
Also doesn't explain why the simulator doesn't actually show them doing anything.