According to Orlik's lecture notes on Seifert manifolds (and the Wikipedia page on Seifert fiber spaces), a mapping torus over a 2-torus is a Seifert manifold if and only if it is the mapping torus of a mapping with trace less than or equal to 2 in absolute value (under the usual identification $\text{MCG}(T^2) \cong \text{SL}(2,\mathbb{Z})$). For the trace $+2$ ones, the Seifert invariants are simply $\{b; (o_1, 1); \}$ for $b \in \mathbb{Z}$.
Also, it is known that mapping tori arising from finite order maps are all Seifert manifolds.
So, the question is: Is there a general way of determining whether or not a given mapping torus over a genus $g$ surface is a Seifert manifold?
Edit: It seems that if one doesn't mind the geometrization conjecture, it is possible to show that mapping tori of pseudo-Anosov homeomorphisms will give mapping tori that aren't Seifert fibered. By the Nielsen--Thurston classification, this leaves us with reducible mapping classes. Can anything be said in general about mapping tori of these?
So you have a fiber bundle $M \to S^1$ whose fiber is $F$. Alternatively, $F$ is the quotient of $F \times S^1$ by the equivalence relation $(x,t+1) = (f(x),t)$, where the monodromy $f : F \to F$ is defined up to isotopy.
By Nielsen-Thurston classification of surface diffeomorphisms, $f$ falls into one of 3 cases :
So $M$ is a graph manifold if and and only if the monodromy is reducible to a bunch of periodic diffeomorphisms. (Essentially, we have proven that in our case, the manifold is either a graph manifold or contains a hyperbolic piece, which is true in all generality if you believe in geometrization). So what's left is to understand if the implication “graph manifold and surface bundle $\Rightarrow$ Seifert-fibered is true (or how wrong it is). I bet the answer is somehow in Waldhausen's Eine Klasse von 3-dimensionalen Mannigfatigkeiten but I don't have access to it at the moment.