Here we will assume that the definition of the Laplacian is $\Delta=\vec{\nabla}^2$, and that $a$ is a non-zero constant.
I) The Lagrangian density
$$\tag{1a} {\cal L}_1~=~ \frac{e^{-t/a}}{2}\left(a\dot{u}^2 - (\vec{\nabla} u)^2\right)$$
has Euler-Lagrange equation
$$0~\stackrel{(1a)}{=}~\frac{\partial {\cal L}_1}{\partial u}
~\stackrel{EL}{=}~\frac{d}{dt}\frac{\partial {\cal L}_1}{\partial \dot{u}}
+\vec{\nabla}\cdot\frac{\partial {\cal L}_1}{\partial \vec{\nabla}u}$$
$$\tag{1b} ~\stackrel{(1a)}{=}~ \frac{d}{dt}\left(e^{-t/a}a\dot{u}\right) - \vec{\nabla}\cdot \left(e^{-t/a}\vec{\nabla}u\right)
~=~e^{-t/a}\left(a\ddot{u}-\dot{u}-\Delta u\right) $$
equal to OP's first PDE
$$\tag{1c} a\ddot{u}-\dot{u}-\Delta u~\stackrel{(1b)}{=}~0.$$
II) The Lagrangian density
$$\tag{2a} {\cal L}_2~=~ \frac{e^f}{2} (\vec{\nabla} u)^2$$
has Euler-Lagrange equation
$$ 0~\stackrel{(2a)}{=}~\frac{\partial {\cal L}_2}{\partial u}
~\stackrel{EL}{=}~\vec{\nabla}\cdot\frac{\partial {\cal L}_2}{\partial \vec{\nabla}u}$$
$$\tag{2b}~\stackrel{(2a)}{=}~\vec{\nabla}\cdot \left(e^f\vec{\nabla}u\right)
~=~e^f\left(\Delta u +\vec{\nabla}f \cdot \vec{\nabla}u\right) $$
equal to OP's second PDE
$$\tag{2c} \Delta u +\vec{\nabla}f \cdot \vec{\nabla}u~\stackrel{(2b)}{=}~0.$$
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[Note added: OP's question was originally cross-posted to mathoverflow and migrated back to Math.SE, so that OP's question appeared in duplicates on Math.SE. This answer (which was composed without knowing of the duplicate entry) originally appeared under the original Math.SE question, but is now moved here to collect all answers in one place.]