For the shuttle to move it needs to have kinetic energy this means that the shuttle will use more energy when travelling as opposed to being stationary. The laws of Thermodynamics tell us that energy is conserved.
Seriously, have you seen the size of Destiny. He's not going to suffocate from methane poisoning due to inhaling his own waste products any time soon. To be extra safe I'd advise him to go down to Rush's quarters to take a dump and be sure to close the doors afterwards.
I don't know the power requirements of the stasis pods I'd assume it's not massive though. It might be worth trawling the transcripts to see if it's said anywhere.
Like I said before Eli would use the stones so he wouldn't be bored at all. He'd probably spend most of the trip on Earth while SGC sent specialists to use his body to fix up Destiny in the meantime.
The one left out of the stasis pods isn't the one left out to die, he's the one who gets to decide which of the others he'd like to eat first. They wanted a 'darker' more edgy side to the show lol