Cloud Atlas is one of my new favourite films, it was just fantastic start to finish. If you don't like movies that make you pay attention and you have not read the book, then you might not be into it as the switching between stories might annoy you, but that wasn't a problem whatsoever for me. Overall I thought it was extremely well made, well paced, engaging and believable. If you're concerned about Tom Hanks, IMO I thought he did very well in this film, the only problem is that he is just so famous/recognisable that the makeup guys had a job to do to stop you thinking "oh there's Tom Hanks again" as opposed to "oh there's <character X> again".
Pi, well, Darren Aronofsky has a certain style. I would say that to enjoy Pi you have to be in the right frame of mind, it is (deliberately) like gently burrowing a needle into your brain, like you are meant to have a headache by the end of it. But don't let that put you off! It just goes to show the mastery of the medium that he has. Not really sci fi, although I suppose it's close.
However, if you are going to watch an Aronofsky movie then the one I would recommend would be
Requiem for a Dream. It has a similar "need to be in the right frame of mind" quality about it because it is not a happy movie, but this is my favourite film of all time in any category, ever. When you watch this film it will really "affect" you. Look out for how the tempo of the film gathers, towards the end it just feels relentless, with no "filler" dialogue scenes to let you relax. When it ends it will feel like you've been holding your breath in the middle of a warzone and have just made it back to base. It's largely down to the drama of the score, part of which you will probably recognise because it has subsequently been used extensively in dramatic trailers for other movies (e.g. LotR: Two Towers, Sunshine, I am Legend).
(Edit: bonus point for Requiem for a Dream is that, if you don't tell her anything about the film, your wife/girlfriend might watch it too as it has Jared Leto in it - in addition to Jennifer Connelly too of course.)
So far I am resisting giving my top 5, it's too hard