My mesh has seams down the arms, legs, sides

First of all, if you are using Milkshape you should make sure that 'autosmooth' is unchecked on the groups page BEFORE importing any meshes.

You can see a screenshot of where that is here, in step 31
http://www.modthesims2.com/showthread.php?t=142305

What has happened is that you did not ruin the shape of your mesh, but by having 'autosmooth' on or using a smooth command - you damaged the Normals - which contain information for how to display the mesh as a smooth, rounded object instead of a bunch of flat triangles.

Also you should not use the milkshape 'smooth' command, because that will do the same thing as autosmooth does. You can use Demon's Tools if you need to smooth a specific spot on the mesh.

If you are using the UNIMESH plugin, you should not need to smooth the seams, the maxis smoothing will be preserved, as long as you make sure that before importing any meshes, make sure that 'autosmooth' is unchecked on the groups page. If you are building entire new parts and adding them to a mesh, you can use Demon's align normals tool (below), which lets you smooth selected parts of the mesh without smoothing the rest.

If you accidentally had autosmooth on in UNIMESH and therefore ruined the original normals (and now have those visible seams) you can get the normals fixer which is part of the Milkshape GMDC Tools by Demon432 and use them to smooth the selected areas of your mesh. DO NOT WELD IN UNIMESH!

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If you imported your mesh with 'autosmooth' on, you have damaged it. The answer is to fix your settings and START OVER again fresh. I know this is disappointing, but once you have fixed your settings, you should not have it happen again - although with each upgrade of milkshape you will need to reset your settings. Be a careful and watchful mesher - you should NOTICE when there are seams visible on your mesh before you've gone and spent a week editing it.

If you really must salvage a damaged mesh, if you use smoothing groups to separate things like hemlines (look at the article about Normals) you can probably use smooth or demon's align tools to repair the ruined normals. You should also consider (once you have turned autosmooth off) importing a mesh and using extended edit to fix the neckline normals to exactly match the Maxis ones, otherwise there will be two shades of skin on your neck - your bodymesh will have one and the head another.

If you are using UNIMESH, stop reading NOW, the next part does NOT apply to your mesh!

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The following applies to edits made with SMD format, BODYCHOP, MESHTOOL, and Wes' 2.6 plugin...

if the Maxis seams are far more visible on your mesh than on the original, you can weld the seams (be sure to just pick the areas you want to weld, you might not want to weld, say, the sharp edge of a skirt or anywhere else you want to have a sharp edge).

There is a mini tutorial with information on how to smooth the seams in XSI Modtool here

Screenshots