There are many department store bikes that have standard components. The one I purchased is such an example. The Denali that one poster mentioned has standard parts as well.

Yes, some bikes at department stores have "non-standard" components. By and large, they all have standard components, though.

Brakes? Check. You'd replace the whole part anyways.
Drivetrain? Check. Again, generally, you don't fix those, you replace the parts.
Bottom bracket? Maybe. YMMV
Handlebars? Most likely. One-offs are more expensive than a current production run that's rebranded.
Cranks? Most likely. YMMV.
Wheels? Probably not, but you might luck out.
Tires? Who cares, just get a new tire that fits the rim. Same with tubes.
Shifters? Most likely. They're pretty much all Shimano, with a few SRAM's on there. Low end of course, but generally Shimanos are all interchangeable. And you don't usually fix shifters, you usually replace them.

Did I miss anything?