I am horribly confused by the cluster of terminology and operations surrounding "change of basis" operations. Finding alternate references on this topic only seems to add to the confusion as there doesn't appear to be a consistent approach to defining and notating these operations. Perhaps someone will be able to clarify just one simple aspect of this which is as follows:
Let $u = \{u_1, \dots, u_n \}$ and and $w = \{w_1, \dots, w_n\}$ be bases for a vector space $V$. Then, necessarily, there exists a unique linear operator $T:V \rightarrow V$ such that $T(u_i) = w_i$. Now, the most natural thing in the world to call the matrix of this operator is the change of basis matrix from $u$ to $w$. Give this operator a vector in $u$ and it spits out a vector in $w$. Now, whether it is correct I don't know, but I've seen the matrix of this operator called the change of basis matrix from $w$ to $u$, reversing the target and source bases. This latter interpretation makes no sense because because it takes vectors in $u$ and produces vectors in $w$! I've seen this interpretation in more than one place so it can't just be a fluke. So...which is it?
The "change of basis matrix from $\beta$ to $\gamma$" or "change of coordinates matrix from $\beta$-coordinates to $\gamma$-coordinates" is the matrix $A$ with the property that for every vector $v\in V$, $$A[v]_{\beta} = [v]_{\gamma},$$ where $[x]_{\alpha}$ is the coordinate vector of $x$ relative to $\alpha$. This matrix $A$ is obtained by considering the coordinate matrix of the identity linear transformation, from $V$-with-basis-$\beta$ to $V$-with-basis-$\gamma$; i.e., $[\mathrm{I}_V]_{\beta}^{\gamma}$.
Now, you say you want to take $T\colon V\to V$ that sends $v_i$ to $w_i$, and consider "the matrix of this linear transformation". Which matrix? With respect to what basis? The matrix of $T$ relative to $\beta$ and $\gamma$, $[T]_{\beta}^{\gamma}$, is just the identity matrix. So not that one.
Now, if you take $[T]_{\beta}^{\beta}$; i.e., you express the vectors $w_i$ in terms of the vectors $v_i$, what do you get? You get the matrix that takes $[x]_{\gamma}$ and gives you $[x]_{\beta}$; that is, you get the change-of-coordinates matrix from $\gamma$ to $\beta$. To see this, note that for example that $[w_1]_{\gamma} = (1,0,0,\ldots,)^t$, so $[T]_{\beta}^{\beta}[w_1]_\gamma$ is the first column of $[T]_{\beta}^{\beta}$, which is how you express $w_1$ in terms of $\beta$.
Which is why it would be the "change of basis matrix from $\gamma$ to $\beta$. Because, as Qiaochu mentions in the answer I linked to, the "translation" of coordinates vectors achieved by this matrix goes "the other way": it translates from $\gamma$-coordinates to $\beta$-coordinates, even though you "defined" $T$ as "going" from $\beta$ to $\gamma$.