The fact that $H_n(S^n,S^n-\{x\})\cong\mathbb{Z}$ is a bit unintuitive to me, can anyone give me some insight?
This is a common fact in any introduction to algebraic topology course, it is achieved by using an exact sequence of pairs and then showing that $H_n(S^n,S^n-\{x\})\cong H_n(S^n)$.
It seems strange to me though.. When I think about $H_n(S^n,S^n-\{x\})$ as the homology group of $S^n$ except removing $S^n - \{x\}$, it seems that only one point should be left, and so the $nth$ homology group should be trivial. I realize that $H_n(S^n,S^n-\{x\})$ is not a "good pair" as Hatcher would say, and that my way of thinking was definitely oversimplifying things, but I was wondering if anyone could shed some light in general onto this for me. Thanks!
I like to think of $H_n(X,A)$ as "trying" to be $H_n(X/A)$. If $(X,A)$ is a "good" pair this is a literal equality, but in general it's more of a heuristic.
If you try to compute $H_n(S^n/(S^n - \{x\}))$, you run into the fact that $S^n/(S^n - \{x\})$ is a two-point space, and turns out to be contractible. My intuition for why the homologies fail to be equal is that $S^n - \{x\}$ "surrounds" $x$ in a way that can't be captured when we quotient it away, because we simply don't have enough points or open sets. The "right" way to fix this is to replace $X/A$ with the cofiber of the inclusion (essentially a "homotopically good version of the quotient"), but I don't think this is very intuitive if you're learning from Hatcher's perspective, so here's a heuristic that won't always work but does give some insight:
It's a general fact that homotopy equivalences preserve homology. In our case, we can contract $S^n - \{x\}$ to $S^n - X$, where $X$ is a little (closed) circular disk around $x.$ The pair $(S^n, S^n - \{x\})$ is then homotopy equivalent to the pair $(S^n, S^n - X)$, so in particular they have the same homology. $(S^n, S^n - X)$ is not a good pair, but intuitively $H_n(S^n, S^n - X)$ "wants to be" $H_n(S^n/(S^n - X)).$ But $S^n / (S^n - X)$ just looks like $S^n$, so its $n$th homology group is $\mathbb{Z}.$
You need to use some sort of excision argument like in the other answers to get a rigorous proof, but in general this heuristic of "replace spaces with homotopy equivalent spaces with a little bit more wiggle room" is a good way of making your intuitive guesses line up with the actual answer.