In some sense, all examples are deformation retracts. If $X\simeq Y$, there is a space $Z$ containing $X,Y$ and $Z$ deformation retracts onto $X$ and also onto $Y$ (see Hatcher, chapter zero).
But there are many examples of a homotopy equivalence where the two spaces don't naturally include one another. So, in particular, they are not examples of deformation retractions. One that I always like is, for $n>2$, where you have $n$ half circles attached at a common base and endpoint (formally, something like $\bigvee_n[0,1]$ with all the ending "$1$"s identified to a common point) and you know by some general nonsense it is homotopy equivalent with $\bigvee_{n-1}S^1$.
A similar example would be that a pinched torus / doubly pinched sphere / croissant is homotopy equivalent with $S^2\vee S^1$, but there is no obvious way to embed one space into the other.
The "difference"? Well, if $Y$ does not embed into $X$ nor conversely, then $X\simeq Y$ cannot be written as a deformation retraction. For me, it's less that there is a difference and more that deformation retractions are just special cases where one space contains the other (and the homotopy has an extra property). Homotopy equivalences, I'll grant, are much harder to visualise as "wiggling space around" when they're not deformation retractions, but ... this is just the general, useful notion.
Maybe the most important point is that the maps $X\to Y\to X$ need not be "faithful", injective, surjective, whatever; in a deformation retraction there is a clean inclusion to focus on, but in general you could have quite weird maps which witness the equivalence.