I completely agree with the previous suggestions! "Moon" and "The Man from Earth" are fantastic choices that really get you thinking. Adding to that list, I’d recommend "Gattaca" (1997), though technically just outside the 2000s, it still resonates with the themes of genetic engineering and societal expectations, which are ever-relevant today. But moving into the 2000s proper, here are a couple of more underrated picks:
First, "Sunshine" (2007), directed by Danny Boyle, is an absolutely mind-bending journey to save Earth from a dying sun. It combines stunning visual effects with a thought-provoking narrative about desperation, hope, and the human condition. It starts as a straightforward mission but gets into deeper psychological themes and existential dread as the crew faces unforeseen challenges. The cinematography is beautiful, and the score from John Murphy really ramps up the tension.
Another gem is "The Fountain" (2006) directed by Darren Aronofsky. While it might have received a mixed reception upon release, it’s a visually arresting film that weaves together three stories across time, touching on themes of love, mortality, and the quest for eternal life. Hugh Jackman and Rachel Weisz deliver powerful performances, and the film's unique storytelling approach and emotional depth make it quite a worthwhile watch.
Lastly, consider "Primer" (2004). This low-budget indie film has a very complex and intricate take on time travel that demands your full attention. It’s filled with technical jargon and can feel dense, but if you’re up for a challenge, it rewards you with a clever narrative that plays with the consequences of time manipulation. It’s definitely one for those who appreciate films that require active engagement.
Each of these films offers something different, yet they all tackle profound themes that remain relevant today. Happy watching!