Has the Isbell–Freyd criterion ever been used to check that a category is concretisable?
I did this once with the category of schemes in response to this question, with help from Laurent Moret-Bailly. But then Zhen Lin Low pointed out there's an obvious concretizing functor. Maybe it wasn't so obvious until we were sure it was there, though. So I suppose this falls under the "useful heuristic" category. In practice, the Isbell-Freyd criterion translated the problem into something more concrete (pardon the pun!) which an algebraic geometer had a sense for how to answer. At the time, I didn't know enough algebraic geometry to answer this question on my own, so translating it into more geometric language which I could ask somebody else was an essential step for me.
It helped that, as Ivan Di Liberti points out in the comments, the criterion is especially simple in a finitely-complete category.
[Answer converted from a comment by Jiří Rosický on another answer.]
Isbell’s criterion is used directly in Libor Barto’s paper Accessible set functors are universal (pdf), Section 4, to show that the category of “accessible set functors” (i.e. accessible endofunctors on $\mathrm{Set}$) is concretisable. A slightly different argument, based on the simpler criterion “regular-well-powered” for the finitely complete case, is used for this same example in Remarks 5.5–6 of Adámek–Rosičký How nice are free completions of categories? (arXiv:1806.02524)
An inverse category can be defined as a category where every $f$ admits a unique regular inverse, i.e. a map $g$ such that $fgf=f$ and $gfg=g$. In [1], Kastl proves that any locally small inverse category admits a faithful functor into $PInj$, the category of sets and partial injections. The proof first verifies Isbell's criterion, obtaining a faithful functor to $Set$ and then one proves a general result giving rise to a faithful functor to $PInj$.
[1] J. Kastl. Inverse categories. Studien zur Algebra und ihre Anwendungen, 7:51– 60, 1979.