Is it bad for one's future career prospects if the PhD thesis topic is broad? As a graduate student in the PhD program (I will be graduating in about 2 months), my research has covered a wide range of topics rather than nailing down one specific topic (super-specialized). In fact, my thesis is broad enough that my current working title is something along the lines of "Toward the Application of Electronic Structure Theory to Solve Relevant Chemical Problems." (Can it get any more general?) There is nothing informative from that title as it completely leaves out details. The problem is, each paper I've published is its own research focus without any connection to the next outside of the fact that computational chemistry was used for each.

I've read in other places that a thesis topic is critical because it is the basis on which you launch your career. Is it bad to look like a 'jack-of-all-trades' person? There must be a better way to handle this.
Coming from a somewhat different field (mathematics), I have seen some theses that were essentially bundles of not-strongly-related papers, each good enough to get published, and considered (by the advisor and the department) good enough to earn a PhD. Ok.

But this is indeed different from "getting a job". From what I have seen, job applicants don't succeed so much with "broad appeal" alone, but also must have strong appeal to a particular research group/interest. Thus, a too-diffuse body of work, especially if described in a fashion that makes it appear diffuse _and_unfocused_, will not get up to the thresh-hold of having a good chance at job opportunities.

To my mind, the point is how one portrays such work. If (in contrast to the situation of the question) the papers really are completely disjoint and unrelated, it is not easy to describe them as fitting together into a coherent research program. If, indeed, as apparently is the case in the questioner's situation, there is a coherence to the body of work, it is very important to re-describe things to emphasized that. "Novel computational methods whose potential is illustrated by making progress in several important problems"? That sort of thing?

After all, presumably/often the author of several papers does have some underlying theme/principle/concept/whatever that is merely manifest in various way ... that may superficially appear very different.

So, in summary, the description of the body of work would best emphasize the common thread(s) underlying the several instances. Although often labels are simplistic, hiring committees do use them, so figuring out how to position oneself among those labels is probably smart. (In effect denying the relevance of admittedly simplistic labels and categorizations is most likely just self-sabotage.)

One's advisor's approval of the body of work as meriting the PhD is a different issue from getting the advisor's recommendations about an appealing coherent description of the whole of the work.