How can I join multiple objects with different modifiers on each one?

I’m modelling a macuahuitl, which is chunks of obsidian embedded in wood. Creating the obsidian required subsurf, displacement, and voronoi, and I had to tweak these individually to get the chunks to look good. The problem is, now that I want to attach everything together, Ctrl+J seems to apply all the processing to each chunk AND the wood, and it ends up looking completely different. Is there any way to isolate the modifiers and textures for each part so I can join them without changing the appearance of each piece?

Ctrl+J joins the selected objects to the active object (last selected object) so the resulting object will only have the modifiers that the active object had.
If you need to apply any modifiers before joining
The Displacement modifier setting can set it to only apply to a vertex group
Subdivision surface modifiers apply to the whole object
The different materials are maintained when joined so different faces however you want.

Mockingbirch, consider parenting or grouping your objects. Here’s a link to the wiki about these…
http://wiki.blender.org/index.php/Doc:2.6/Manual/Modeling/Objects/Groups_and_Parenting
… and here’s a vid about instancing groups…