Let $M$ be a smooth compact closed manifold. 
Let $u \in H^1(0,T;H^{-1}(M)) \cap L^2(0,T;H^1(M))$ be a solution of
$$u\_t - \Delta u - u = 0$$
$$u(0)=u(T)$$
satisfying $\int\_M u(t) = 0$ for all $t$. Is there any way to show that $u$ must be zero (i.e. solutions are unique)?


The problem is the $-u$ term. We have Poincare's inequality in this but it does not help much.
I would appreciate not using a method to do with eigenvalue problems since this PDE is a simplified version of what I am working on. 



Uniqueness of weak solutions of a heat equation
Your claim holds true if and only if $-1$ is not an eigenvalue of $\Delta$.


If there is a nontrivial function $v:M\to\mathbb R$ with $\Delta v=-v$ (then necessarily $\int\_Mv=0$), then $u(x,t)=v(x)$ solves your PDE with all conditions but does not vanish identically.


Suppose then that $-1$ is not an eigenvalue.
Then it follows that the line $-1+i\mathbb R\subset\mathbb C$ is in the resolvent set of $\Delta$.
Because of the boundary condition the solution $u$ can be thought of as a periodic solution (w.r.t. time).
Then it is very convenient to take the Fourier series of $u$ in $t$:
$$
\hat u(x,s)
=
\int\_0^Tu(x,t)e^{2\pi its/T}dt
$$
for $s\in\mathbb Z$.
Since $\widehat{u\_t}=-\frac{2\pi is}{T}\hat u$, the PDE becomes
$$
\left(\Delta+(1+\frac{2\pi is}{T})\right)\hat u
=
0.
$$
Notice that the equations for different Fourier components decouple.
Since $-(1+\frac{2\pi is}{T})$ is in the resolvent for all $s$, we have $\hat u=0$ and consequently $u=0$.


Even if we do not assume that $-1$ is not an eigenvalue, we know that the spectrum is real.
Therefore the above argument shows that any solutions $u$ has to be constant in time ($\hat u(x,s)=0$ when $s\neq0$) and thus an eigenfunction of the Laplacian — and the eigenvalue should come as no surprise.


