In Pressley and Segal's book Loop Groups, they define a "basic inner product" $\langle-,-\rangle$ on a simple Lie algebra to be (minus) the Killing form scaled so that $\langle h_\alpha,h_\alpha\rangle=2$ where $h_\alpha$ is the coroot associated to a long root.
[Aside I believe there is some terminological confusion possible here: they surely mean $h_\alpha$ to be an element of the Lie algebra, rather than an element of $\mathfrak{t}^*$; Terry Tao defines a coroot to be such a thing, appropriately scaled. But others take a coroot to be a rescaled root, for instance Wikipedia.]
They give the examples of $\mathfrak{su}(n)$ and $\mathfrak{so}(2n)$, which are $-\mathrm{tr}(XY)$ and $-\frac12\mathrm{tr}(XY)$, respectively. To avoid confusion, this trace is taken in the defining representation, thinking of these as matrix Lie groups.
But I haven't been able to find a source that gives the basic inner product for $\mathfrak{so}(2n+1)$ or $\mathfrak{sp}(n)$, where the latter are given as $n\times n$ quaternionic matrices. Once one knows the appropriate matrices $h_\alpha$, then it is obvious. And it is sufficient to know these for low ranks, for instance $\mathfrak{so}(5)$, since then matters stablise.
I tried asking for these actual matrices over at M.SE, but despite rather a detailed answer, I still have no joy, as it presumes a lot of "common knowledge" of Lie theory I don't have, and also is slightly loose with terminology and suggestions. I was hoping for something super explicit like writing out the analogues of the Pauli matrices. This seemed like material too basic for MO, but despite a lot of searching, no lecture notes or textbook I've found actually gives this information! Nor have I found student exercises that ask for them. To me this seems like a perfect example of what MO was intended for: a place for researchers to ask colleagues about a basic fact they need from an area they are unfamiliar with. So I'm cutting my losses, forgetting the exercise of trying to work this stuff out for myself, and asking outright:
What is the basic inner product on $\mathfrak{so}(2n+1)$ and $\mathfrak{sp}(n)$?
My motivation is that eventually I'm going to be doing physics-style calculations, and need explicit representatives for absolutely everything. So a characterisation in terms of anything else is insufficient: I want a formula. A reference to a place where this is recorded in the literature would be the best answer, but I despair that such a thing exists.
Best Answer
Section 4 of
Gawȩdzki, Krzysztof; Reis, Nuno, Basic gerbe over non-simply connected compact groups, J. Geom. Phys. 50, No. 1-4, 28-55 (2004). ZBL1067.22009.
lists, in an absolutely concrete way, the simple Lie algebras realized as matrix Lie algebras, together with all roots and coroots. From these you can get the normalization.
For example, let's look at $\mathfrak{so}(2n+1)$. Let $e_i$ be the $(2r+1)\times (2r+1)$ matrix with a block $$ \begin{pmatrix}0 &-1\\1& 0\end{pmatrix} $$ on the diagonal at the $(2i-1)$th and $2i$th position. Then, the roots are the matrices $\pm e_i \pm e_j$ for $i\neq j$ and $\pm e_i$, and the coroots are $\pm e_i \pm e_j$ for $i\neq j$ and $\pm 2e_i$. You can check that $\mathrm{tr}(X^2)=-4$ for all coroots $X$. Thus, the basic inner product for $\mathfrak{so}(2n+1)$ is $$ -\frac{1}{2}\mathrm{tr}(XY) $$ just as in the even case.