If you can create matching hash pairs at will, the interesting attack in binaries is to distribute one that acquires a trusted reputation under the shared hash, then at a later date replace it with the problem one.

Not too bad of a risk if diverse hashes are often used and people promptly move away from any hashes that demonstrate collisions; could be a nasty surprise if the collision is privately discovered and sprung at an inopportune moment, or people keep trusting an older hash after collisions start appearing in the wild.