For file management and quick adjustments I use Aperture.
Recently got DxO, which has some nice features, though sadly doesn't interact with Aperture. So, as Apple is discontinuing its software, I might switch to Lightroom.
Cleanup happens with Photoshop.
For heavier work I like using After Effects. Yes, that's a film tool, but I do love its workflow. It is resolution independent, so can do photos just as well. All filters are completely non-destructive and can be readjusted anytime. There's proxies for fast work yet full quality render. And all files are linked, which keeps projects very small so they can be used as presets, where I just exchange the source images and adjust filters.
Also, I know it rather well and have way more plugins for it than for Photoshop.