From memory:
- In ME1 Liara has different voice lines, depending on when you decide to recruit her.
- In ME2 if you wait too long before the final mission, (most of) your crew dies which will affect the story of the last game.
- In ME2 you have to talk to your crew regularly to get them to unlock special options or abilities.
- Talk to Conrad Verner all the time in 1 and 2 and you'll get a reward in 3.
You can always compile from scratch, compare the checksums or use the version you compiled. In projects this large people usually do this, and there's a certain level of trust that these checks have been performed.