In my study of groups, rings, modules etc, I've seen the three isomorphism theorems stated and proved many times. I use the first one ( $G/\ker \phi \cong \operatorname{im} \phi$ ) very often, but I can't recall having ever used the other two. Can anyone give some examples where they are used in a crucial way in some proof?
For clarity, let us say that the 2nd one is : $(M/L)/(N/L) \cong M/N$ under the appropriate conditions, and the 3rd one is $(M+N)/N \cong M/(M\cap N).$
As Boris and Alexander have mentioned, both these theorems are used a lot in the study of normal series, and particularly soluble groups.
One basic example of this is the following. A group $G$ is metabelian if it has a normal subgroup $N$ such that $N$ and $G/N$ are both abelian.
Theorem Any subgroup of a metabelian group is metabelian.
Proof Let $G$ be a metabelian group with normal abelian subgroup $N$ such that $G/N$ is abelian. Let $H$ be any subgroup of $G$. Then $H\cap N$ is a normal abelian subgroup of $H$ and $H/(H\cap N)\cong HN/N$, which is a subgroup of $G/N$ and is hence abelian. Thus $H$ is metabelian. $\Box$
The same sort of idea could be used with induction to prove that any subgroup of a soluble group of derived length $n$ is also soluble, of derived length at most $n$, although I don't think that's the standard proof.