@Iron Pipes: Keep in mind that they will never output into a wooden pipe, so you can place one of those where your wood comes into the pipe. Then, you should be able to place a lever next to the iron pipe- on means furnace, off means pulverizer. Or whatever.
@Biofuel: Throw water, saplings, and fertilizer into a fermenter to make biomass, then send the biomass into some Stills. With water, you'll need slightly more than four stills per fermenter, however, if you squeeze the apples for their juice, and use the juice in the fermenter instead of water, you'll get more biomass per sapling, with the need of about six stills, if I remember correctly. I would recommend having saplings first get sent into a juice-powered fermenter, and if that fills up (because you ran out of apple juice), send them into a water-filled fermenter.
@Machines Filling Up: Put a diamond pipe on the machine in question and tell wood, saplings, whatever to go in, it will try to put the items in, but if they won't fit, it will pass them on to the next pipe. A diamond pipe adjacent to an inventory will never drop an item, if there is a direction with no items specified. Just to be sure that nothing goes backwards, it's good practice to place a cobblestone or another item that will never show up in the network in the pipe on the direction where items enter the pipe.
@Pulverizing Apples: Diamond pipes. Have one send apples one way and wood somewhere else.