With a siege, as soon as food starts getting scarce, the hoodlums will start coming out to prey on the weaker folks. Lots of small riots for the PC's to help quell. Then, if you have a PC that can create food - what happens if they can create food/water for ten people, and 1000 people show up?
Disease will start to take a toll. A great way to get the point driven DEEPLY home is if a character has an ability/spell to cure disease and is overwhelmed by parents trying to get their kids cured - way too many for them to actually cure - REALLY emphasize the horror and hope on the parents' faces.
As people die, what happens with the bodies? As the PC's travel through the town, describe having to step OVER bodies in the streets.
Another great idea is for the enemy to have a limited quantity of "special" ballista bolts that scream as they fly over the town. If one in 100 drop a tiny greek fire bomb, every time the population hears the scream, they'll panic. This is akin to the Buzz Bombs the Nazi's used on London in WWII - VERY effective for psychological warfare. They do very little damage, but destroy the population's mood.
This is a WAY neat idea, and I may be stealing this for my own campaign for future use!! Welcome aboard!