Last I heard, ISBoxer will work if you run ISBoxer (and export to Inner Space) from Windows and run Inner Space in wine. IS does require WoW to be in Direct3D mode, but it should work. You may need to copy a font or two from a windows install for Inner Space fonts to work right, as well as d3dx9_37.dll.

The ISBoxer program is only used to make configuration changes, and it didn't work in wine last I heard because it's a .NET 2.0 program.

I imagine other multiboxing programs would probably work under wine as well