1. Use .DDS textures. my tutorial has all the vanilla textures extracted as both .DDS and .TGA
2. UTF editor is used to making edits to CMPs or MATs for many purposes. for example, you can embed textures into the CMP itself instead of having the need of a mat file, or in your mat file, you can edit it so you have glow maps (self illumination) or transparency, etc. you can also create wireframes in that, and is also ideally used in certain cases of sur splicing amongst other things.
3.best file format would be OBJ. i use that, and it works perfectly for me.
4. i think i uploaded a pack which has 1.8.2 version of milkshape, you should try and get that + the importer/exporters.
5. CMP is for any type of model. 3DB can be used for stuff like models, or icons etc and generally cant be hitboxed like a CMP is, it requires a wierd way to making the hitbox via UTF editor iirc. MAT files are for the material files, and SUR is for hitboxes indeed.