The last two versions of AVID Media Composer support 3D editing natively...w/o 3rd-party plugins.
FCP has actually 3 options...
1-Cineform Neo 3D, which is expensive (around $2400!) but real-time.
2-Dashwood 3D Toolkit, which is a suite of plug-ins for FCP...very full-featured, ($1400).
3-Dashwood 3D Toolkit LE...limited functionality, but CHEAP! ($99)
The Dashwood tools use FX-Factory, and free versions (15 days) are available for download.
Tim also has some great tutorials online...google 'em!
Booth FCP & AVID are pretty much industry standards...Sony's VEGAS 10...the latest version also edits 3D natively, but the interface is a bit different from other NLE's...