I guess it depends on what you do with your phone, but for me when I rooted and flashed a custom ROM/kernel I saw such a significant improvement in battery life (about 2x) with my typical daily use (which is moderate to heavy) that I haven't felt the need to get a higher capacity battery. I mean, no, it's not going to improve the battery life if I watch videos all day, but checking email, surfing, or even listening to music really doesn't require the Evo to run at full horsepower like it obviously does when stock.
I know that not everyone necessarily wants to mess with the internals that much for risk/warranty reasons, but when the 3,500 mah eBay battery overheats, puffs up, and breaks your Evo, do you think Sprint/HTC is going to cover that under warranty?
I can afford the Sprint $60 one, but like others have mentioned here, I really don't think I should have to pay more money to Sprint to get the best performance out of their phone. It should come to me that way (they should hire the developers of the ROM and kernel I'm using). I also don't like the idea that a new battery door (which may or may not fit like OEM) will cause me to lose my protective case for my phone. I don't think Sprint is going to honor/accept my excuse that my phone broke when I dropped it because their extended battery prevented me from using my protective case.
Anyway, just wanted to throw that there for people who are thinking about rooting/flashing their Evo's -- improved battery life is typically a benefit of that or at least it definitely can be if you opt for the right kernel.
Good thread though -- it's good to know what's out there, especially good to know what Sprints up to, as they always slyly put solutions like this out to correct "problems" with the phones post-release.