well for a start I'm shocked, shocked that Quatermass and the Pit didn't make the final list. That said, the first two were easy - Star Wars changed everything for SF. Everything. The release of SW was a watershed moment for the whole genre. At the time I wasn't much of a fan of it - I was already a SF fan and also a fantasy fan and I didn't really like the way the film mixed the genres up: it seemed neither fish nor fowl - looking back I can see I was too blinkered.
The Matrix was such a great idea and so well made - every shot just seemed perfect with ground breaking SE to boot. My jaw dropped.
then to choose between the rest... 2001, well, you know, no doubting Kubrick was a genius but I always found his pacing to slow. District 9? I can only assume it made the list because its so recent - instantly forgettable minor movie. Terminator 2 - great thrills and spills action adventure, great monster, but too star-driven, take away Arnie and what have you got? Planet of the Apes - good idea, good lead, but I didn't think it was particularly well made. Clse Encounters I enjoyed but that Speilburg surburban cosiness and the special effects ending spoiled it for me.
So the choice came down to between two Ridley Scott movies, both set in corporate dystopias - each in their own way saying that the future is like now, only more so - for me Blade runner was a little too de-focused whilst the focus on Alien was intense. One of the first movies to put gothic horror in space, a truly alien alien for a change.