I am on a mac and I wonder if there is really a big difference in the quality of my footage if I use Neo Scene rather than converting the video in iMovie or Final Cut Pro?
Yes you need to install "Perian" its free. I use NeoScene all the time! it is great and the quality is much better then Apple Intermediate Codec. best $129.00 you can spend if you have a Mac and a HMC 150 in my opnion.
I use NeoHD and have encountered annoying problems but so far its doing the job for now.
Basically it's converting it to a 4:2:2 colour space which is good for VFX and colour grading. I do notice the difference between raw AVCHD footage(4:2:0) and Cineform's codec 4:2:2.
If you have Final Cut, you might as well just use ProRes, it's like Cineform's codec but now with even more options.