For Retail / Airlines, you often remove Rent because it is a major expense and one that varies significantly between different types of companies. The same way you would value a company: by looking at what comparable apple trees are worth (relative valuation) and the value of the apple tree's...
This is a pretty broad question, and it's not clear what your specific area of interest is here, but I'll take a stab. The first thing to note is that Apple has two "sides" to it: retail and corporate. I don't know anything about the retail sid...