Well, it really depends on the mod. First, you usually have to unzip the archive file (probably either .zip, .rar, or .7z) or run a .exe. If you had an archive file, you usually either paste the files into the appropriate folder or use JSGME (which automatically does it for you if the mod has the right file tree). Sometimes, files need to be edited as well - this is almost always easily done with a simple text editor like Wordpad or Notepad. One thing though - if you have to replace files and are not using JSGME, make sure you save copies of the files you are replacing; I usually save at least one blank installation of both SHIII and SHIV just in case I need some vanilla files back later but it will suffice just to save the files which are going to be replaced. If you are using JSGME, it will automatically rollback the files for you if you need to do so.
EDIT - I've been away for awhile though, and I'm not sure if JSGME is ready for SHIV yet.
Maybe someone else can add some more specific instructions if they like.:hmm:
Also, instructions usually come with each mod though and are fairly straightforward.
Hope at least some of this is useful.