It has been a while since I've read my old issues of Amazing Spider-Man, but I don't think my question had ever been addressed in the books that I've read.

If Peter's parents were spies, why were Aunt May and Uncle Ben always poor? Wouldn't the government have offered assistance for raising the son of two of its deceased agents? Didn't Mr. and Mrs. Parker leave any inheritance for their son?

I think in the early ASM annual, Peter's parents were believed to be spies for the Red Skull and he unveiled that they were actually counter-spies working for the USA. Whether or not that info was actually passed along anywhere I can't remember, but if Peter is the only one who "knew" the truth, then I wouldn't be surprised that the government didn't pay for Peter's upbringing if his parents were believed to be traitors.

I also think there is an Untold Tale or something with his parents teaming up with Wolverine, but I haven't read it.

This shit has been retconned so much it's hard to tell what is true and what isn't anymore.