The equation to solve is:
$\displaystyle x\frac{\partial u}{\partial x}+ \displaystyle y\frac{\partial u}{\partial y}+ \displaystyle z\frac{\partial u}{\partial z}= \displaystyle xyz$
Applying the Lagrange-Charpit equations to $x$ and $y$, and $y$ and $z$ we trivially get $\frac{x}{y}=C_1$ and $\frac{z}{y}=C_2$. However I have a problem solving
$(1) \displaystyle \frac{x}{dx}=\frac{xyz}{du}$
This leads to
$\displaystyle xdu=xyzdx$, and
$\displaystyle du=yzdx$, integrating
$\displaystyle u+C_3=xyz$
This would mean that the solution to the original problem is
$F(\displaystyle \frac{x}{y},\frac{z}{y}, \displaystyle u-xyz)=0$ with an arbitrary $F$.
And indeed $\displaystyle u=xyz$ satisfies $(1)$. But the third function in the actual solution should be $3u=xyz$ which in turn does not satisfy $(1)$.
What am I missing?
Your Lagrange equations are statements about the relation of x,y,z,u along a curve in 4-space. This is somewhat hidden in the notation, but is brought out clearly in the solution by doraemonpaul. So when you say that $x/y=C_1$, that means along one of these curves; for the pde, x and y are still going to be independent variables. So when you say that your equation (1) leads to $du = yzdx$, that is still a statement along the same curve. So your deduction $u+C_3 = xyz$ is not correct. You could write instead $du = yzdx=\frac{x}{C_1}\frac{C_2x}{C_1}dx$, and integrate to get $u = \frac{1}{3}\frac{x}{C_1}\frac{C_2x}{C_1}x+C_3 = \frac{1}{3}xyz+C_3$. In general I think it is better to include the $t$ parameter as doraemonpaul did, because the idea of the method of characteristics is to use these parametrized curves to transfer Cauchy data into the space.