Mostly they'll be .png or .gif files, made using Photoshop or a similar digital art program.
If you don't have any, GIMP is a good open source image editor which can be downloaded from here.
There's loads of good tutorials out there on the web to help you get started if you just google around a bit, and you'll probably get an answer if you post any specific questions on the forums here (assuming someone here knows the answer )
It's not that simple sadly.
While I cannot give you the full details on 'how' to make them, Freelancer uses a very, VERY sketchy icon type with the extension of .3db - One which isn't very easy to make properly.
Perhaps resources around theStarport may help you on that one.
Creating the icon itself can be done through any image editing software. GIMP, Photoshop, etc.
Converting it so it actually can be used ingame, now that's another story..