Have you ever tried to access the Wall Joins tool where you have only two walls meeting?  Such as in a T intersection scenario like this:

On my Revit 2014 system, the Wall Join modifiers will not activate in the Options bar when clicking on the above join.

However, if you add a bit of temporary wall, like this:

You can now access the Options for the Wall Join.  Set your option, then delete the temporary wall.

This workaround allows you to set the “Don’t Clean Join” option on a 2 wall T-intersection…

Another tip – if you have trouble selecting a particular Wall Join, select two or three walls that participate in the join and then use the sunglasses to Temporary Isolate Elements.  You should now be able to select the proper join.

Standard Casework families can not join geometry in the project environment, but Generic Models can.  There are various opinions on how to handle this.  From RFO:

Aaron Maller (using Generic Model, non adaptive):
Ours are generic models, non-line based, and we join geometry. It reports quantities correctly but conservatively, since a mitered corner reports both full lengths. But i prefer it that way. AC’s are nice, but since they havent made one that is multiple point with point number dictated on the fly, im not making 7 different families so i can have a 2, 3, 4, 5 and so on.

Alex Page (Generic Model, but using subcategory):
Ours are Generic models (on a subcategory called Casework) so we can successfully use the join tool, and line based for ease of use… 

Steve Stafford (Casework, adaptive):
ah youze guys are chickens I made this one in less than five minutes from scratch. Not much more work than the old in-place deal. Make a few versions and you’re “done”.

Read more:
2012: Clever Countertops

Old 2006 post on AUGI, listing the then ‘joinable’ categories:
It seems to be that only elements of some categories can be joined. Using the default Revit Building template, these are the categories that can be joined:
Ceilings
Columns
Floors
Generic Models
Mass
Roofs
Structural Columns
Structural Foundations
Structural Framing
Walls 

via 
http://forums.augi.com/showthread.php?42732-Casework-Families-Geometries-Don-t-Join

The question remains – what do YOU do to solve this problem?

And can you find a ‘current’ and complete list showing the categories that can Join Geometry in the Project Environment?

When you use the Join Geometry tool in Revit, you may notice that it sometimes just doesn’t seem to ‘work’. You do everything right, join the two adjacent surfaces – and there is still an ugly join line!

The problem is that Revit only wants to join surfaces correctly IF they are the same material. You could go into each object (floor, wall etc) and make sure all the materials are the same. However, the quick fix is shown below:

  1. Use the Paint tool to apply the same material to the two faces you want to join.
  2. If you have already ‘joined’ the surfaces, you need to unjoin them from each other. With walls, the easiest way to unjoin two objects is to physically disconnect the wall using grips (I do this in 3D). Revit will give you a warning – and you can then Unjoin the elements.
  3. Now, pull the objects back together, so they are in the same plane and they meet at a clean edge.
  4. Use Join Geometry again between the two surfaces – now that they are the same material, Revit is happy to join them properly, and it all works beautifully!

In short, Revit wants joined surfaces to be the same material before it will join them properly.