My bounty for this question expires soon :)
Edit: in regards to the bounty offered, what current research trends use the Jordan canonical form?
If one takes a second course in Linear Algebra — or a graduate level Linear Algebra course — one typically learns about non-diagonalizable operators and the Jordan canonical form.
However, where does the Jordan canonical form show up again in later, more advanced mathematics? All I hear from applied mathematicians is that the Jordan canonical form is useless in practice (in academic research). If it's not useful in applied mathematics, is it an important tool in pure mathematics? If so, in which areas of pure mathematics?
In brief, the Jordan normal form and various of its siblings are ubiquitous in mathematics, whether labelled "pure" or "applied" or whatever. This is not to assert that numerical computation of literal Jordan forms is worthwhile, or stable, etc. In fact, as in my earlier comment, the very instability can play a very practical role in looking at families of linear systems that "go close" to the kind of degeneracy that non-trivial Jordan blocks depict.
For that matter, Jordan form is just a special case of the structure theorem for finitely-generated modules over principal ideal domains, such as $k[x]$ where $k$ is a field. Again, yes, in both a strong-topology sense and in a Zariski-topology sense, having non-trivial "Jordan blocks" is anomalous, but it can happen, and things "nearby" start to behave less stably.
Various non-normal compact operators on Hilbert spaces also can have non-trivial Jordan blocks. For example, the Volterra operator $Vf(x)=\int_0^x f(t)\,dt$ has this behavior.
The importance of rationality and algebraic-group-theoretic aspects of Jordan form in the theory of algebraic groups was already mentioned. This is a big deal, after all.
In general, "failure of semi-simplicity" is an awkward thing, and is to be proven not to happen (if that is the case). Failure is manifest in too-extensive non-trivial Jordan blocks. For example, "Galois representations" (that is, repns of Galois groups on various cohomologies of algebraic-geometric objects) "should be" semi-simple, etc., but this requires proof.
The case that a second-order ODE degenerates to have two closely-related solutions is an instance of a non-trivial Jordan block.
In complex analysis and algebraic geometry, representations of $\pi_1(X)$ as "monodromy groups" raise the potential issue of non-trivial Jordan blocks.
And so on. "Jordan block" is an essential descriptive notion, nearly everywhere. People who say it's "useless" are either just playing rhetorical games, or are pretty ignorant of serious mathematics.