When children learn about the basic elements of the sentence -- subject, predicate, object -- they practice on simple sentences, beginning with the subject. Therefore, it is not uncommon to read the sentence, "There is food in the fridge" and consider "there" the subject. For this reason, when you are dealing with such sentences, omit "there." The sentence becomes, "Food is in the fridge." You can then ask, "What is in the fridge?" and spot "food" as the subject.
When you're dealing with a polar question -- a question that can be answered with a yes or no -- convert it to a statement first. For instance, the question "Did John do his homework yesterday?" must temporarily become "John did do his homework yesterday." From this point, you can follow the standard procedure and ask "Who did his homework?" to find the subject.
Prepositional phrases are those starting with a preposition and ending with a noun or pronoun object. For example, "near my house" is a prepositional phrase you can include in a sentence, such as, "The bank near my house is safe." Don't be tricked and use the object of the prepositional phrase -- house -- as the subject. Instead, omit it altogether and go through the standard process: "The bank is safe." "What is safe?" "Bank" is the subject.
Certain sentences -- direct requests and commands, for instance -- may not explicitly state the subject. "Clean the table" or "Give me a call tomorrow" are simple examples of such sentences. On such occasions, you can understand the subject from the context: search previous or later parts of the text to see who is the person the character is talking to. When the command is oral and directed at you, or is targeted toward a reader, the implied subject is "you."