Suppose we are in a proper closed model category and consider a commutative square $$ \begin{array}{rcl} A&\to& B\\ \downarrow&&\downarrow\\ C&\to&D \end{array} $$ in its homotopy category. This square is canonically isomorphic in the homotopy category to a square in which all morphisms are morphisms of the model category (we assume here to have (fixed) functorial factorizations such that all this can be done nicely). Hence, w.l.o.g. the square above is a commutative square in the model category.
If we (functorially) factorize the morphism $A\to B$ into a cofibration followed by a trivial fibration like $A\to B'\to B$, we can form the categorical pushout $P$ of $$ \begin{array}{rcl} A&\to& B'\\ \downarrow&&\\ C& \end{array} $$ There is an induced map $i:P\to D$ in the homotopy category and one can define the initial square to be a homotpy pushout square if the map $i$ is an isomorphism in the homotopy category.
If one considers now such a homotopy pushout square $$ \begin{array}{rcl} A&\to& B\\ \downarrow&&\downarrow\\ C&\to&D \end{array} $$ in the homotopy category with morphisms $B\to E$ and $C\to E$ such that everything commutes, there should be a (unique?) morphism $e:D\to E$ in the homotopy category obtained by the construction above.
My question is: Why isn't this construction the colimit in the homotopy category? I have heard that homotopy colimits are not categorical colimits in the homotopy category. Does it fail with the uniqueness of the morphism $e$? The existence of $e$ should be sure. Does one have at least the existence of an induced morphism (in the homotopy category!) for general homotopy (co)limits?
I think you don't even have the existence of $e$.
The problem is:
As for the first question, in general the answer is that a morphism from $A$ to $B$ in the homotopy category is a sequence of maps of the original category
$$ A= A_0 \stackrel{\sim }{\longleftarrow} A_1 \longrightarrow A_2 \stackrel{\sim}{\longleftarrow} \dots \stackrel{\sim}{\longleftarrow} A_n \longrightarrow B $$
where the ones going to the left are weak equivalences.
In general, it's difficult to tell when two such sequences are equal. The best think you can have is that your class of weak equivalences admits a (right, left) calculus of fractions. Then, arrows in the homotopy category are sequences of length $2$
$$ A \stackrel{\sim}{\longleftarrow } A_1 \longrightarrow B $$
and equality between two such sequences means that some diagram made up from four triangles is commutative. In general, equality involves bigger commutative diagrams in the original category. For more information, see Dwyer, Hirschhorn, Kan, Smith, "Homotopy limit functors on model categories and homotopical categories", AMS Math. Surveys and Monographs, 113.
So, try now to say what's the meaning for two such arrows (sequences) starting from your $B$ and $C$ and ending in $E$ to form a commutative diagram in the homotopy category. Then, try to imagine how this could imply the existence of some $e: D \longrightarrow E$.
EDIT. Maybe I can add another point of view. If $\cal{C}$ is a model category, then its (Quillen) homotopy category (obtained inverting its weak equivalences) $\mathrm{Ho} \cal{C}$ is equivalent to the (classical) homotopy category $\pi_{cf}(\cal {C})$; i.e., the category whose objects are the fibrant-cofibrant ones and maps are homotopy classes of maps of $\cal{C}$.
So, this $\pi_{cf}(\cal {C})$ allows you a more specific representations of maps of the (equivalent, Quillen) homotopy category: here, they are "real" (homotopy classes of) maps of $\cal{C}$, not unmanageable sequences.
Even in this equivalent homotopy category, the problem remains: when you have two (classes) of maps $B \longrightarrow E$ and $C \longrightarrow E$, making your diagram commutative in $\pi_{cf}(\cal {C})$... "Commutative" in $\pi_{cf}(\cal {C})$ means commutative up to homotopy in $\cal{C}$. And it doesn't matter if your objects are fibrant-cofibrant and your morphisms cofibrations: from the universal property of the push-out in $\cal{C}$ you cannot deduce the existence of $e: D \longrightarrow E$ if you have commutativity up to homotopy in the diagram involving $B \longrightarrow E$ and $C \longrightarrow E$.