Roscal -
They say English is the hardest language to learn. But your English is waaay better than my French

I use Flowtherm at work, but can't use it for waterblock analysis as my company would tend to frown on such endeavors

Here at home, I'm limitted to doing things the old fashion way with equations and spreadsheets for fluid analysis as I couldn't afford commercial CFD software for personal use

(also using my experience to look at general design problems, knowing what the flow will look like as a result of the block features)
BTW, the technical term for the "limit layer" in English is the
boundary layer. Oh, and you get the "Understatement of the Year" award for your comment "the coupling between temperature and other parameters because it's much more complicated"
Regarding the perpendicular slots on the surface - in one project at work I found slots with an minor angle in the direction of flow worked better overall for that type method
Brad -
As Roscal described, you almost always have a boundary layer in fluid flow. However, you can greatly reduce its size by various techniques. The two major determining factors are the velocity of the fluid and the surface structure. In general higher velocity means a thinner boundary layer and more turbulent flow. The other way (surface structure and channel features) can get a bit more complicated, but as I've said before, there is a decent volume of research in that area.
A good common example of the effects of surface is a golf ball. The boundary layer and fluid flow characteristics are what help determine how far a golf ball travels through the air (air in this case is the fluid). That's why golf balls are dimpled - to help reduce the drag created by the boundary layer (although the goal in a golf ball is different than what you want in a wb - to use a similiar method in a wb you would want rounded
protrusions rather than concave dimples).
In the case of a wb, we want increased turbulence near the surface which also causes an increase in the flow resistance. One example of a minor improvement to turbulence is Fixitt's sandblasting of the surface (note to Fixitt - shot peening would work better for
that method).
You get to a trade off point in a wb though - if you increase it too much, your flow rate for a lower pressure pump starts to drop off, and you could end up with a net loss in the heat transfer coefficient do to the lower Reynold's number (which is an indicator of the turbulence level).
The surfacing on the floor of the newer Maze3 is an attempt to address this issue.
If you look at the middle pic of the Maze2, you'll notice that one of the thicker boundary layers it at one of the worst possible locations - the inner wall over the core area (just after the first 180 turn from the center inlet, the wall closest to the inlet). The other major not so great "weak spot" is the low velocity at the back wall of the inlet and the back half of the floor under the inlet. (the greatest temp delta is in the area just over the core, so that is where you want the best heat transfer).
Fixitt - if Roscal is so inclined, it would probably help him if you had a 3D model already done up in Autocad (you might have to export it as an IGES model - not sure how well Cosmos handles regular Autocad files)

If you only have a 2D model of it, and Roscal is willing to look at it for you, I might be able to help (I could convert it to a 3D model with Rhino without too much effort - mainly depends upon what types of 3D model files his version of Cosmos can handle).
JD - have you ever seen a bit that you could create a knurled type surface on wb passages?

Regarding the bit you found - an important piece of info : you do
not want to create any surface channels that are parallel to the flow as this will contribute to a laminar flow along the walls.