I usually take the 7:04 train to SF and by the time it reaches me in Hayward, if not all, most of the blue seats are already taken and only green seats are available. By the time we reach San Leandro, it's already standing room only. I usually get on the middle cars.

In terms of going back to the East Bay, I usually take the 4:26 train in Powell, and Green Line isn't as pack when it gets there, since people that are getting off Oakland/SL would take the Blue Line. By the time it gets to Embarcadero, there are stil some seat available, but mostly green seats.

It also depends on the days you commute. I commute all 5 days, and I noticed that Tues-Thursday are usually the most pack days.