Hey all,
I saw the post on flow maps this morning, unfortunately I do not have photoshop so I did some googling on how to do the same thing with gimp… not much came up but I did stumble upon this cool little app, its awesome! FlowMap Painter – teckArtist
Very easy to make flow maps(actually even easier than how it is explained with photoshop 
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BTW: It works fantastic under wine as well 
Agreed, The flow map painter is a good tool if you just want to do something quick, but not necessarily accurate.
The most accurate way to generate them is to generate them mathematically in Houdini or Maya. I use Maya to make flow maps for Particle Systems/VFX based on Fluid Simulations, and I use Houdini to make level-based Flow Maps similar to the way Valve did theirs for Portal and LFD2.
ImbueFX has a great tutorial series on Flow-Map creation for Particle Systems: Here (Website Currently Down)
And Community member RedBox did a great .PDF on how to make them with Houdini for level-geometry: Here
sometimes i take the manual/slow approach 