A lot of the uses for item customization are simple and obvious, like simple personalization - a Progia with a custom case and cute keychains, or a pistol notched for every Judge you've taken down, or a motorcycle helmet covered in totally rad flames and lightning bolts and whatnot - but I think more outlandish uses of the feature would make for some pretty surprising and inventive cases, like a super-modified LiteTerm turned into a Google Glass-style head mounted display, a mechanic's toolbelt reconfigured into a high tech arm-mounted multi-tool, a glowing glass orb that works as a flashlight, or a whole category of James Bond-esque "things disguised as other things" for especially tricky folks.
I understand that something like this would be a huge undertaking, but I think it'd be a great vehicle to let characters get their hands on unique or personalized gear with a minimum of GM / coder intervention. Signature items of these kinds would also make for great trophies, for the more cut-throat among us - lighting a cheap cig in the Mix with some high level corpie exec's custom engraved, albiet blood-stained lighter might just enhance the flavor a bit.