Hello I am wondering if there is any tool that creates an automatic polygonal merging between two separate objects, , I am not just talking of attaching an object to the other but like have to meshes and get them closer and when enough close merge the two models into one like if I put together two drops of mercury or the like .....

Boolean does this, but it can be messy. It won't create a soft transition between the two, but it will delete triangles where the two interpenetrate. It's messy because a boolean often creates long thin triangles, or holes, or it just refuses to work. You can improve the results by making sure both meshes are "closed" and making sure they have an even vertex distribution.

The cleaner way to do it (but more time-consuming) would be to Attach one to the other in Editable Poly, then delete the overlapping triangles, then use Bridge to fill in the gap.

ProBoolean is pretty clean.
Boolean is mostly for compatibility i think

yeah I meant ProBoolean. It's an improvement, but it still has problems.

I think he's looking for Blobmesh...

...mmm cryptic puzzles. I think he's talking about something like
Weld + Threshold (but automatic).

What is Blobmesh ?

Metaball lives!

You might want to check out 3DCoat and more specifically the docs about voxel sculpting. Not exactly what you are describing, and not animatable, but it might be just as good.

I think Blender has good metaballs tools.

Like the functionality of the symmetry modifier but with two different objects? That's a tricky one indeed.

ah yes now that i read more carefully.. he confused me with the polygonal meshes..
metaballs is one thing butit doesn't take any object and merge. there are special tools for that.

maybe this could help you do what you need?

http://www.solidthinking.com/InspiredNav.aspx?pid=4