Well which game do you want to mod first of all.
Milkshape can be used to make models but you will need a good paint shop program to texture the model.
MicroSoft Excel can be used to edit the ship specs for the most part. You can use a standard text editor if you are extremely carefull.
You will need some of the Taldren tools which can be found at
www.starfleetuniverse.com which are mainly used for SFC3.