First off, great mod. I enjoy it a lot.
Did a search for "chemical" and checked the already suggested suggestions thread, and turned up nothing. So apologies if it is in planning, or has been suggested and I missed it.
A Google search for "minecraft chemical mod" and "minecraft chemistry mod" turned up MineChem as the most relevant mod. Appeared to have a full periodic table but no real purpose other than possibly serving as a base for other mods.
Also, this is a bit more of a general category suggestion (and in fact more of a 'is-this-planned?' question than anything else), so no specific recipies or such mentioned.
Chemical Engineering and Chemical Process Plants
I believe an untapped avenue for Industrial Craft is that of chemical reactions and chemical engineering. In most modern process plants (even large furnaces) large chemical process sections exist. These are typically geared towards concentrating ores (sorting the desired from the unwanted), before other processes such as electrical smelting (gold, iron, etc.) or electroplating (copper).
Your typical chemical reaction (if oversimplified) has some standard parameters that IC² can use to simulate a simplified (and more generic) chemical process with:
1. Heat in reaction (in degrees Centigrade), changing based on reaction (Exothermic [heat-making] or Endothermic [heat-eating]). Some reaction may require player to remove heat (cooling fans, coolers, etc.) or add heat (Heaters, etc.), in essence keeping it within a specific margin.
2. pH level (Again, pH levels are typically important for both getting a reaction to work, and nasty side effects at both extremes.)
3. Concentrations (A simple use for this would be to indicate how much slurry (solid-in-liquids, or gunk) you have).
4. Efficiency (Not directly manipulated. Essentially reports back how well you are maintaining the reaction).
N/A. Would personally like to see more 'build-it' recipes (like railcraft choke furnace) for chemical tanks/reactors/mixers/etc.
Since this would be a rather new avenue, I would suggest to first start with a simple chemical reactor (I.e. big tank for stuff to happen in). Adding sufficient water to the tank, along with reagents (chemicals that fizzle and make stuff happen), along with sand or dirt or cobblestone (i.e. common blocks), and getting the heat, pH and concentration right, it starts leeching some useful ores from the reaction, along with producing waste (useless except perhaps for recycling).
As a poor 'no-thinking' example: The reactor can leach copper from sand when setup for it, and kept at pH (3.1 to 4.1, best 3.5), and Heat (140°C to 240°C, best 155°C).
Each sand block added ups the concentration by 0.1%.
Each copper ore leached out drops concentration by 4% (one copper ore per 40 sand or less if closer to optimum reaction values), drops heat by 10°C, increases pH by 0.1, and produces twenty waste.
Some other items can lower or raise pH (like clay lowering pH or... or... not sure really).
EU can be converted into heat added (heaters) or heat removed (coolers).
Reactor chamber may require way to monitor Heat/pH/Concentration and output signals at user defined levels (Hi level and Lo level for each of the three).
Essentially the same as heap leach processes in real life. I'd keep recovered ores ratio low, as not to discourage mining.
(Starting point idea probably overlaps in function with EE, but that is another mod and does not require maintaining some form of reaction to obtain results).