They're admittedly not applications most users run every day, but many multimedia applications (audio processing, encoding, decoding) is mostly done with hand-crafted instrinsics, the same goes for video stuff.

In an even more niche area (high-end VFX apps, like compositors, renderers) SSE/AVX intrinsics are used quite a bit in performance-critical parts of the code, and auto-vectorisers can't yet do as good a job (they're pretty useless at conditionals and masking).