It's probably been mentioned already but, I'm a great fan of Anarchy Online myself.
It's a MMORPG but the entire focus is about customizing yourself, you pick your own weapon regardless of breed or profession (though you may be less proficient), you use implants to pick your augments out of three slots (or symbiants, pre-made and pay2play only), for 13 specific areas of the body (eye, head, ear, right arm, chest, left arm, right wrist, waist, left wrist, right hand, legs, left hand, feet).
You're pretty much an enterprising immigrant, the year's 29'487 and you can pick sides with Omni-Tek, a megacorporation that owns the rights to the relevant planet Rubi-Ka to mine empty for the precious mineral Notum (which is used as a mana-like resource for nanoformulae, like spells) and the Joint Clans which are locked in a struggle with Omni-Tek wanting to make a home on Rubi-Ka and stop the mining operations.