Mesh: Weird transparency, holes, strange display
If the mesh looks perfectly intact inside the 3D graphics editor and simpe, but has holes or strange display issues in bodyshop or the game, the cause is probably a bad or missing bone assignment.
The bone assignments need to add up to 100%, each vertex *must* be assigned to a bone or bones.
Unimesh Bone Assignments
If you are using the UNIMESH plugin, there are some rounding errors that can result in bone assignments that add up to 99% or 101% when they are imported. You must fix them, or you will get little display quirks where sometimes the hands look like they are on the hips, other times they look in the hips as you rotate your sim, and so on. (if you look at the pjs pic below, you'll see the hands and hair act oddly in the different shots)
Go to the VERTEX menu and select "Sims 2 Unimesh Fix
Underweighted Bones" (be sure to choose the correct command, there are 2 similar commands on that menu - and if you don't have that command, go get the most recent unimesh plugin and install it)
If there were underweight bones, a popup will display saying how many were fixed. Click OK.
IF Unimesh does not find underweight bones, and your mesh still looks odd in game, go check the individual bone assignments in the problem area by hand. At least once the numbers added up to 100%, but there was an odd bone assigned that caused the problem.
Hair With Holes
If your hair has holes or odd display at the edges, and underweight bones fixes did not change it - it could be the layering values are not correct, or layering order - hair is very fussy about that. This mostly applies if you added layers, deleted layers, or massively moved layers. See Hair and Beyond
for more info.
New Mesh Parts Showing the Wrong Side, or Only One Side
Mesh faces have sides - only one side is visible in the game. If you make a new semi transparent skirt layer, for instance, it has to have an inside and an outside. For more info, you can look at this thread. http://www.modthesims2.com/showthread.php?t=61852
Layering also matters (in a way similar to hair meshes) when dealing with semi-transparent mesh parts (aka alpha meshes). To properly line such skirts, you will need a body mesh with 3 groups. If you use solid alphas (allowing for hem changes, but not transparent meshes) then you can put both the skirt and lining in the same alpha group.