(this track):
Jon Hopkins - Open Eye Signal - YouTube
You have great taste! Jon Hopkins is a true legend. My favorite track on that album is Collider.
The bass:
I think it's several oscillators of saw-waves at different octaves, the ADSR is a little quicker decay and a lower sustain, maybe a little release time too. He seem to have assigned the ADSR to the velocity, so the decay starts at a higher amplitude making it pop more when he hit the notes harder and make a much softer sound when not hitting the notes as hard. Seems like he have done the same thing a little with a lowpass-filter making it cut more, and also more smooth when hitting more softly on the notes, and then when he hit the harder notes it instead have a higher cutoff frequency and also more of an envelope-shape (in this case: a quicker decay and low sustain) making it sound almost like a pluck/stab-sound.
The pads at 2:00:
To me it sounds like 2 synth-layers.
The first layer sounds like a classic soft-pad, a sawwave with a smooth unison playing in a thick chord with a lot of lowpassfiltering playing at a lowe volume to create a foundation.
The second layer is the classic voicepads playing in different notes more for the purpose of getting a nice ambience more than a nice melody.
These 2 together both probably go through a reverb
plugin with a bright reverb and a long decay and he have probably also removed a lot of the dry-mix from the pads to make very airy.
Further on there are small synths that fade in in short times, like at 2:26 a squarewave with some lowpassing through pretty much the same reverb settings fades in.
Just my guesses though.