This may have seem liked a textbook question to answer and there lay the complexity in answering the question. Thank you all for attempting to answer; R Rajesh has given some common business situations.
We come across many such business situations - the one that we are all aware of is "pre" and "post" improvement comparison in a DMAIC project. Very clearly it is an apples to oranges comparison, as the process itself has gone through changes. This comparison is made possible by using indices such as Cp, Cpk, Pp, Ppk or Sigma Level.
There are times when Balanced Scorecards across different divisions are compared - the metrics of the divisions may be completely different, hence an apples to oranges comparison. %age attainment to goal is another way this comparison can be made possible.
One may also reason that accuracy rates, defect rates, coefficient of variation can also help make apples to oranges comparison.