Ok, here it goes. First of, love the mod, its an amazing addition to minecraft and combined with buildcraft adds a lot of possibilities to express ones creativity!
One of the biggest appeals of the mod to me is addition of new machines and resources. Its always fun getting your first macerator up to process all the ore you have been saving!
I have a few suggestions on how to further enhance that process as well as adding new and exciting stuff to industrial craft.
I apologize in advance for not including the crafting recipes for my suggestions, I will leave it up to you to implement it in accordance with what you consider balanced.
1. New resource, unobtanium. Same rarity as gold and located at the same depths. Requires iron or better pickaxe to mine. Unobtanium will not be crafted into anything, but instead, used to enhance other ores. One example I thought of was modifying macerator to accept unobtanium in the bottom slot (in a way that matter generator accepts scap kind of). If unobtanium is present in the machine then the ore is enriched, yielding 2x or 3x more dust when its macerated. Since unobtanium is not abundant it could be used to enrich ores like iron or gold to get more out the limited resources you may have.
Unobtanium can also be used to enrich uranium, through macerator or perhaps whatever other means seems more appropriate. Enriched uranium ore can then be combined with living matter to create bioethiric energy source. Living matter is just what it sounds like, "living" blocks suck as flowers, mushrooms, trees, etc.
2. Bioethiric energy source. Crafted like advanced machine blocks and circuits, these energy sources can be used to create a new machine capable of converting energy into life. The most useful example I can think of is a tree growing machine. Load sapplings into the machine and it will automatically grow the trees around it. Sapplings are only used if the tree is grown, if there is no room for a new tree then nothing happens. Also, Bioethiric machine would require electricity to operate as well as a nearby source of life, such as flowers. The more flowers you have directly adjacent to the machine itself, the less energy it would require. I dont know if a tree growing machine is balanced or not, but it would definitely make life a lot better 
3. Scanner. A scanning can be programmed to "recognize" certain blocks in nearby proximity. The scanner will be a crafting component for a more advanced machine, lets call it a harvester that will have a "Target" and "Action" parameters. A target is basically a block that is inserted into the machine, for example wood (to link it up with my previous suggestion). The harvester would then need an "Action" parameter on what to do when it detects the "Target" block. So in this particular case we want it "cut" the wood down so we could use a chainsaw in the second slot to specify that if it scans wood nearby it will use "chainsaw" to cut it and then store it in nearby chest.
Suggestions #2 and #3 would allow for automated wood harvesting, kind of like auto miners. To compensate for balance, bioethiric life generator could require large amounts of energy to "produce" the life.
To add more possible examples, scanning / harvesting can also be programmed with sand and shovel for example to collect all nearby sand and just sand. The kind of shovel used (iron, bronze, gold, etc) could determine the rate at which it is collected and the tool can be used up in the process, requiring additional tools. Basically as long as the tool matches the resource in the harvest settings it would use the tool to collect the nearby specified resource. Can run off of batteries to avoid having to wire.
Another use for bioethiric life generator could be to act as a creature spawner. If you insert porkchop into the machien as a parameter, after it has drawn sufficient amount of energy it would spawn a pig. Wool would spawn sheep, leather would spawn cows, and bones would spawn zombies and skeletons, gunpowder could spawn creepers. Place a tesla coil nearby and whoala, you could an automated mob spawner / resource harvester (with obsidian pipe):)
