I don't see why the cars the engines are in from the factory matter in a "Best Engine" debate. OK, so some people don't like the AWD layout of a DSM, some don't like the FWD of an SRT-4, who gives a shit? How about swapping them all into a Caterham 7 to level the playing field, if you need to muddy the waters.
I'm going to say it's a tie between the SR20, 4G63, and 3S. They can all put out ridiculous power and they all have their advantages and disadvantages.
As for the 4G63 rev issue- I have read many accounts from reliable sources of running to 8500 rpm on the factory stock valvetrain with no problems. I've communicated with a guy running to 8800 with aftermarket cams being the only reason for lifting the valve cover, no problems, no signs that the valvetrain can't take it. Probably the only thing making it difficult is the dsm tranny- but this isn't a comparison of transmissions, it's an engine comparison.