What does "do" mean in "What do I do?" I think it means "What do I usually do?", but I don't know why anyone would ask what they usually do. Does it mean something else?
Do can occur both as an auxiliary verb and as a lexical verb. In your example, it is an auxiliary verb in the first instance and a lexical verb in the second instance. The lexical verb, I assume, presents no difficulty. It means things like perform, execute, achieve, carry out, effect, bring to pass.
As an auxiliary verb, do is used to form questions and negatives. When a question begins with a word like what, and that word is not the subject, auxiliary do (or does in the third person singular) is placed before the subject of the clause. This applies when the lexical verb is do, just as much as it does with any other lexical verb.
In a clause such as this, do, as ctype.h has suggested, can mean should, but it does not necessarily do so. The question could, for example, be a response, seeking clarification, to the question ‘What is your job?’
In this case, the first do means should. Therefore, What do I do? means What should I do?. If someone asks What do I do? they are not asking what they usually do, they are asking what they should do.
While this usage is common in colloquial English, it should usually be avoided in formal English; it would be better to say What should I do? unless you are quoting someone.
Additionally, there is a similar question, What do you do?, which usually means What job do you do? or Where do you work?. This, like the other question, is also informal.