They all communicate the same idea, but they would likely be used in different contexts. Sentences one and two are identical, except that "set up" is more informal than "arrange." I personally use "arrange" in work/business settings and "set up" in informal settings. For most scenarios I can think of, "arrange" is formal and would sound a bit robotic in casual conversation.
The use of "work out" in the final sentence implies that there is a need to come to an agreement. Let's say two people are trying to find a time to meet. Person A proposes "Monday at 1PM," while Person B proposes "Monday at 4PM." Person A can only meet at 1PM and Person B can only meet at 4PM. This is a really important meeting, and they need to find a time to meet soon. So, one of them says to the other, "Let's work out a time to meet." They talk and realize that they are both free on Tuesday at 9AM, so they move their meeting to that day and time.