There are ALL sorts of things to buy for your ship, and when you buy the basic items, you get more advanced versions. Plus there are some purely cosmetic things to do to your ship, too! All upgrades are paid for in raritanium. Don't obsess too much about raritanium, you can easily get as much as you could possibly want, and will soon have all the upgrades possible plus be able to change your ship's color every 5 minutes if you want to.

Weapons and Armor
triple boost acceleration engine 15
fusion laser cannons 30
electro mine launcher 10
fast lock missile launcher 20
torpedo launcher 10
advanced shielding system 20
nuclear detonation device 60
hyperspace warp system 45

Upgrades
multi torpedo launcher 20
ultra charge shielding system 40
mega mine launcher 20

Making your Ship Pretty
hi lift wings 5
heavy ordinance wings 5
orxon green 5
bogon blue 5
drek's black heart 5
lombax orange 5
blargian red (original) 5

Ratchet and Clank 2 Going Commando Walkthrough