Individualism
When readers are first introduced to Nicholas, he is attending university. He's at an age of self-discovery, made even more profound by his parents' recent deaths. He takes up writing poetry and reading the French existentialists. He looks to distinguish himself as an individual among his peers by appealing to ethos and snobbery, such as his founding of "Les Hommers Revokes." As time wears on, it brings a great deal of changes for Nicholas as he grows and matures. Through all of this, however, he maintains a resolute commitment to individualism.
This is ultimately what costs him his relationship with Alison because he is unwilling to submit himself to the designation of roles within a longterm relationship. He feels the need to be free, to be special. When he discovers Conchis' poetry book on the beach, Nicholas is certain he has found a kindred spirit -- someone who understands his erudite propensities. In the end Conchis takes advantage of Nicholas' eagerness to distinguish himself in order to manipulate the boy for his psychological experiments.
Paranoia
Understandably Nicholas is suffering from rather severe paranoia by the end of the book. He has no clear sense of what is real and what isn't. Even events which preceded his meeting Conchis, like his relationship with Alison, are suspect because she was participating in the experiment as well. Did Nicholas' parents even die? He's uncertain. Consequently, he carries around a liberal distrust for his perception as well as of people in general. Although he is actively paranoid, Nicholas is correct to think that way. He has good reason to remain suspicious for sometime after this invasive affair.
Cognitive Dissonance
In his research, Conchis is attempting to observe the human mind's ability to resist temptation. He wants to prove that any man can be pushed to violence, though this may not be his ultimate goal with the experiment. While they spend time in conversation, Conchis tells Nicholas story after story which loosely depicts cognitive dissonance -- the denial of one's beliefs or the statement of one, preferable belief which a person does not truly believe. Perhaps the epitome of these stories is when Conchis is forced to choose between taking one man's life himself or allowing all the men on the island to die as punishment for his refusal. As he says, he couldn't take the life, yet he places Nicholas in the same position with Julie/Dr. Maxwell. Nicholas is forced to decide whether or not his conviction not to physically harm a woman is sincere or not in the face of the psychological torture she's put him through.