For this, you kinda have to let it be a free market. Look at WoW, even Mojang's Scrolls.
It's the only way to account for almost... Everything. That's economics for you. Though you have to put in restrictions to prevent inflation. The free market concept will allow for farms to substantially decrease the cost of certain items. Iron, etc. will become relatively cheap and highly accessible to new players. This is a good thing. It'll reduce start up times, increasing the growth of your server greatly.
It's nice because there can be no monopolies. Play it by ear and adjust things accordingly. Adopt the American style of economics. The less interference, the better. Unless you are absolutely sure something needs balancing, let the 'invisible hand' do its work.
If you put too much work into making things systematic, it will fail. Let shopkeepers decide the price. Overpriced goods will not sell and those wanting to get rid of excess by reducing cost, will also increase supply.
What I'm getting at is, don't control the market at all unless you have to. If some resource is exploitable through farms, the prices will adjust. If some resource is scarce, the prices will adjust. Watch for horders, though they aren't necessarily a bad thing either. It'll help you identify what is valuable and scarce in the server. You can make adjustments accordingly for that (i.e. Have a server-run shop that sells scarce goods at a premium. This will also help with inflation, hopefully for obvious reasons. This is basic economics.)
Additionally, if you do the server-run shop (where it is okay to make goods via creative or whatever. It's a balancing strategy for the server, unless you care about being king of your own servers economy. Seems stupid.) You will cause horders to either match your premium price (preventing inflation) or sell their goods at a reduced cost to compete (just as good).
All in all, there are pretty simple solutions to most problems. If you have any issues feel free to message me, I'll try my best to come up with solutions that are manageable, though I am by no means an economist.
Additionally (I'm just going to keep adding ideas like this as I think of them.) You can use the deflated credits earned by the server-run shop as starting credits for newbies:
1.) It'll help them get started
2.) It'll allow for all the cheap goods to be bought, since they are just starting and may want to spend their free credits that way
3.) It'll help you decide what is fair for a starting amount. If you see a significant increase in credits being spent on premium goods, you can inject a lot more credits back into the system like this.
4.) It'll help you decide when to decrease the price on premium goods.
Personally, I view having an economy as a way to encourage creativity and specialization. Some people might specifically go for creating starter machines (generators, electric furnaces) and supplying them to newbies. Some might specialize in creating GT machines. You can even sell these ready made items for a premium as well.
1.) It'll reduce the demand for crafting specific items that are scares, re-mediating any scarcity problems.
2.) Once again, selling things for a premium reduces inflation
3.) It'll encourage other players to compete by selling those machines cheaper.
I think by simply having your own server-run shop that adds scarce goods into the server (out of thin air, I suppose) you can already begin to manage the servers economy without oppressing the server directly.
Just remember to listen. Listen to what people have to say and don't become ignorant either. This is an active job, since we already as a society have devoted so much resources into something called the "economy". It could be fun though, adding a new dynamic to the server. It'll also assist with growth and encourage new players to the server, since start up times are usually the worst. Nobody really likes that stage in the game, at least I don't.
Lastly, you can also go around to shops and buy their goods, if you feel there is an inflated status on the supply of a particular good, that you'd like to see its price raised. Buy all the shops out and leave it at that. It'll decrease the supply for that good, while still rewarding those who put the time into farming those goods. It's also another way you can invoke the invisible hand. Simply dump those items into NEI and call it a day.
Though be careful. Nothing has linear effects on the economy, so you need to be careful when implementing the above strategy. Only do so when you see an inflation that effects game play. (i.e. 10 stacks of iron going for one credit. That'd make it too easy to start.)
Which adds another point. People should be able to sell stuff to the server-run shop for an extremely low price. As per the example above. If everyone has billions of iron, but want something else, they can sell all their iron to the server-shop for super cheap and turn it into currency, then into something they need. This will help to re-mediate, once again, the problem of inflation.