I have the following direct system of finite-dimensional C*-algebras:
$$\mathbb{C} \to \mathbb{C} \oplus \mathbb{C} \to \mathbb{C} \oplus \mathbb{C} \oplus \mathbb{C} \to \mathbb{C} \oplus \mathbb{C} \oplus \mathbb{C} \to \mathbb{C} \oplus \mathbb{C} \oplus \mathbb{C} \to \cdots$$
where the first two maps are $\begin{pmatrix}1 \\ 1\end{pmatrix}$ and $\begin{pmatrix}1&0 \\ 1&1 \\ 0&1\end{pmatrix}$, and all the other maps are constantly $\begin{pmatrix}1&1&0 \\ 1&0&1 \\ 0&1&1\end{pmatrix}$.
First of all, am I right in thinking that the first two maps have no influence on the direct limit? And secondly, is there an easy way to describe the resulting algebra?
You are right: When taking a direct limit like $$A_1\overset{T_1}{\longrightarrow}A_2\overset{T_2}{\longrightarrow}\cdots,$$ the first elements of your direct sequence do not matter. In fact, you can take any subsequence $(n_k)$ (and compose the maps appropriatelly to get a directed sequence $A_{n_1}\to A_{n_2}\to\cdots$) and you still get the same direct limit. You can show this using the universal property.
As for what is the direct limit in your case, we have to make a guess somehow. Essentially, direct limits work in the following way: When the $T_1$ are injective, we may identify $A_i$ with its image $T_i(A_i)$ inside $A_{i+1}$, so we have a sequence $A_1\subseteq A_2\subseteq\cdots$. "Taking a limit" in this case would mean taking the union of all $A_i$, which is an algebra (and put an appropriate norm and close to get a C*-algebra).
Now suppose we have the same algebra over and over again: $$A\overset{T_1}{\longrightarrow}A\overset{T_2}{\longrightarrow}\cdots,$$\ and each $T_i$ is an isomorphism. Then identifying $A$ with its image under $T_i$ yields $A=A=A=\cdots$, so the union is again $A$.
Now to make things formal: Suppose $A$ is a C*-algebra, $A_i=A$ and and $T_i:A_i\to A_{i+1}$ are isomorphisms as above (it's useful to leave the indices). Let's show that $\lim(A_i,T_i)=A$. For this we need to find morphisms $\psi_i:A_i\to A$ which satisfy the universal property. Set $\psi_1=\operatorname{id}$ (this is the identification of $A_1$ with $A_1$), and for $i\geq 2$, set $\psi_i=T_1^{-1}\cdots T_{i-1}^{-1}$ (this is how we identify $A_1$ inside $A_i$). Then I'll leave it to you to show that these $\psi_i$ satisfy the universal property.
In particular, the direct limit in your example is $\mathbb{C}^3$.