First it depends on settings, i.e. with or without a market. With market I have done some measurements (it's about selling a resource to gold/iron/coal) (the calculation you find on http://forum.kozacy.org/jedzenie-vs-kamien-vs-drewno-vt3758.htm) - basically: at the beginning you go all for food (since you need it for ups (barracks & mines) (of course you do food upgrades) (the needed wood/stone you can mostly get from selling coal/iron/gold) after some time when you have the axe upgrade - you can move half of the people to wood if you want to have many stables when you rich enough for stone upgrades - do it - these give best results - then move almost all peasents there (leave some for food to avoid famine) instead of going for stone - e.g. if you go XVIII quickly - you can go for XVIII food upgrade (it's a bit worse than stone: 7000 vs 9000 but still very good) Without market - I'd say 40% food, 40% wood (due to stables), 20% stone. At the beginning you might move some peasants (probably a bit more to stone) depending on the next building you want to build Note: these assume ~5k starting resources, no ships (for this you need much more of wood)
I believed that wood was better at the beginning since it only needed one upgrade and had better selling price than stone and food.
