My system is the following:

1. Add any VFX needed to any specific clip in Cyberlink Power Director.

2. Once step one is completed for all clips that apply, I open all my video clips into Windows Movie Maker.

3. Add all sound FX and music.

4. Add all titles and credits.

"THAC XVII” Entry • YouTube Channel • I voice act

I workout everything with the audio first, assembling the entire audio track then following along while I animate. It helps me visualize the direction of the film. I usually spend quite a while then in post production fine tweaking everything, until I feel it's right (or I run out of time).

After I stumbled upon the Dragonframe 4 beta, I found out that it would support Linux.  Now that it's released, I've moved all of my workflow over to Linux and have had to change a few things.  I used to do all of my post-production in After Effects and Audacity.  Now, I'm using Blender, Ardour, and Natron.  They're all free and worth a Google.

I've done a little bit of test footage with them and figured out the following workflow:
- Cut and composite each individual shot in Natron and do the visual effects there
- Splice every .PNG sequence in Blender and render out as .MP4
- Create and line up the sounds in Ardour
- Render out again with Blender, but this time combining the previous .MP4 with the mixed down .WAV from Ardour

I am still unsure where to put color correction/grading in here.

Feel free to continue to post your workflows.  I'll continue to monitor this thread and ask questions.  Thank you to those who already offered their expertise!

I try to do as many VFX in shot as I can, for example attaching objects to each other to make them look like they are flying instead of having to do a whole bunch of masking work (the best example of this is in the third part my short Harry Potter series ). If you reduce the speed to 0.25, you can see that the snowballs are always attached to a brick during flight, which saved lots of time spent masking things later. The amount of VFX editing that i have to varies, as things like Star Wars brickfilms take a lot longer than Minecraft brickfilms, due to all of the lasers, explosions etc. Anyway this is the usual order of things:

1. Put all clips into the right order, duplicate any parts and cut any scenes that I either don't like or ones which have noticeable issues (the latter however are mainly done during filming so I can reshoot them while I still have everything set up, but occasionally some slip through my original check)

2. Do any VFX work (lasers, masking etc.)

3. Add all SFX, music, and record all of the voices (I know lots of people do this before they start animating, and I should probably do the same, but I've always been able to record along with the animation without too many major issues. However, I have done all the voices first this time for my WW1 animation

4. Add all Titles/Credits

Out of my own interest I have made some notes on the average time taken for certain parts of production (bare in mind that i work at 15fps):

1 second of animation: 45mins (of course this varies a lot, depending on the complexity of the scene)
1 second of masking: 75mins
1 second of speaking: 30 seconds (I usually take 3-5 takes before getting it right, but I have previously done up to 10-15 takes to get it right)!
1 second of VFX (lasers, lightsabers etc.):
1 page of script: 35mins
1 page of storyboard: 25mins if very rough, 50 mins if it isn't rough
Setting up a scene: 30mins
Deleted scenes/Used scenes ratio: 1/3

I would recommend doing the same or at least getting to know the time taken for tings like this as it has helped me with planning what time I need to get things done