Cocoa and Carbon are two different APIs software developers use to write programs. Cocoa is only available on Mac OS X, while Carbon is available on Mac OS X and Mac OS 9. Carbon is very similar to the API available on older versions of Mac OS (hence most applications are ported to Mac OS X using Carbon, although some people do write new applications from scratch using Carbon), while Cocoa is similar to the API used in NeXTSTEP and OPENSTEP.
What does this mean for the average Mac user? Not a whole lot. Cocoa applications can take advantage of a few more system features than Carbon applications (although that's rapidly changing), but are potentially slower than Carbon applications. I'd say don't worry about whether an application is written using Carbon or Cocoa since it doesn't affect the usability of a program in the long run.
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