It's harder to names ones that do, really. It's easy to find some "alternative" to most famous software packets, but despite people repeatedly naming all the same programs (known to pretty much anyone interested anyways), none of them can replace, say, photoshop.
So, out of my head (and, yeah, all of them have "alternatives" no serious user would ever switch to):
Ableton Live
Adobe Photoshop
Adobe Premiere
AutoCAD
Microsoft Office (Excel in particular)
Google Calendar (self-hosted)
VisualStudio of Jetbrains IDEs
> Jetbrains IDEs
The Community Edition of IntelliJ, at least, from which all the others derive (I believe) is open source.