Simulation category

It would be nice to be able to save particle settings, such as for hair, and settings for cloth, as custom presets stored with Blender.

I would love to have more functions in the explode modifier, for example making fractures after a image and also make the exploding mesh thicker so that pieces dont look 2d (maybe should be in a different modifier like shell modifier).

I think this would be great for Blender when doing vfx jobs.

Example:
http://www.free3dtutorials.com/userimages/salek/bc_Using_Fracture_Files/bc_Usin g_Fracture_Files.swf

It would be nice to be able to have different fluids interact with each other instead of just combining into one. but then we would also need to be able to have different materials for different fluids.

http://graphics.ethz.ch/~thuereyn/ntoken3/pubs.html

Nils has done more excellent work on fluid sim. and smoke.
View the link above.

ie baking from the command line

As we all know Blender is growing bigger and better. But in my opinion I think it lacks many good vfx tools that other 3d apps got. Lets say for example:

Fracture modifier:
Used to split up a mesh into pieces defined by a image/texture
http://www.free3dtutorials.com/userimages/salek/bc_Using_Fracture_Files/bc_Usin g_Fracture_Files.swf

Shell modifier:
Makes single faces 3d, like the script solidify in Blender but as a modifier. I think this modifier should also have an option of wich textures to use for newly created faces.

Explode modifier:
Improve the explode modifier. I think it would be great if there were a button wich if pressed only explodes loose parts in a object. In that way you can premodell each piece that should go flying.

Particle System
The particle system today is really great, but I think it needs better collision detection when using objects (or exploding pieces) as particles.

These three modifiers could be used in something like this:
If you have a plane that you are going to shatter, you could first apply the fracture modifier and break it up into realistic pieces based on a image (maybe a broken glass). Then the explode modifier to make the pieces go flying (with "only loose parts" button checked), and at last the shell modifier to thicken the pieces and make them look 3d.