I like the d100 idea. Here is something I've come up with for an example. Let me know what you think. I use the normal system like characters with 3d6 (or 4d6 drop lowest) because it's familiar and people know that 10 is average with no special modifiers either way. My cousin and I came up with it this afternoon over email while working... opinions? This is a simple cut and paste...
---------------------
For running a town I'm going to use 6 stats and then different things you can do will raise or lower it. IE, building a new dock or roads will raise the infrastructure. Tell me what you think...
Population - how fast the city is growing/shrinking
Wealth - how rich the townsfolk and city is
Military - how big and how fast they can react to things
Infrastructure - quality of roads, docks, etc.
Culture - fairs, temples, events, etc.
Loyalty - how willing they are to obey their leaders. (people were VERY willing to obey Stalin)
Figure that 10 is "average" just like for character stats... Below 10 is below average for a town it's size. It's also fairly abstract but you'd use it for dice rolls. So if the population is at 5 or -3 then maybe you'd roll 3d6 every 6 months to see how many people die or move away. If wealth is at 6 you might say that the treasury is declining if you pay all the bills and upkeep, although you could cut the salary of employees or sell-off things to make ends meet. Again, not real hard numbers but a good abstract.
Here is the example town of Weston (population 50-75) from NeMorens Vault. The one you'd be in charge of if you want to.
Weston:
4 population - the town is shrinking fast (-3 modifier), the reason why is the point of the quest.
5 wealth - they're nothing but farmers and lumberjacks with little/no remaining external trade. But everyone has a job and food, just no cash money. However jobs and food is plenty for most.
1 military - nothing but level 1 commoners with their axes and shovels, no organized militia at all (which is where you come in). Perhaps the occasional wandering ranger, but nothing organized.
7 infrastructure - located near a large trading bay, fairly close to a trading road, mines, lumber, etc. It was once rich and all the mines, fish, and trees are still around, but no people. Things are breaking slowly and instead of fixing the mill the miller just moves away to a new town if his place has a serious breakdown. Lots of abandoned buildings, but to a new settler it's better then starting fresh. This is the highest stat for sure since the area used to be prosperous.
4 Culture - no temples or organized events, etc. Sometimes a cleric of Ehlonna (to be changed in Kalamar) stops by to worship, etc. They do have a tavern however...
0 Loyalty - No leaders, he died without an heir and his manor is empty. The neighboring town serves as judge when they feel like it but it's not worth it to them to act as any official authority or protect them from harm.
-------------------------------------------------------------
Like it? I like it since they'll be shooting for 10's as quick as possible to at least be competent and start turning a profit into the coffers. IE, an adventure to help out a cleric might lead to the Cleric making a temple in town and thereby increasing culture. They might fork over 300gp to repair the local bridge to increase infrastructure, curing NeMorens curse will probably bring population up to 8 since people won't be dying of disease anymore, etc.
I figure with all 10's the town will be constant in size, everyone will have food and a job, there will be merchant traffic and goods to trade that a normal person might need, there will be appropriate temples to worship at and the town has means at it's disposal to deal with local bandits.
Dang it! Thats me ... 
