Museli

http://thetekkit.wikia.com/wiki/Water_Strainer It can be used like a geothermal generator, but for water, and plugged into your main energy network to add a bit of extra power. Give it redstone power, and it destroys any water that exceeds its storage, making it work well as a filter. Another way to filter out water would be to set up a separate water tank, then use a waterproof diamond pipe to send water into that tank, by putting a water bucket into the pipe's filter slot. EDIT - having looked at that wiki page again, it seems that using it as a filter now crashes everything - my info was a little out of date, sorry. Diamond waterproof pipes should still work as a filtering method though.

Oil and water mixing isn't so bad, guys - just put a water strainer somewhere in a straight section of your oil pipeline, pop a redstone torch (or other redstone power source) next to it, and it'll destroy any water that tries to come through your pipeline, while leaving any oil untouched. There's other ways to pump ocean oil while filtering out water, but that's the one I like.

Butwanna - you may want to try sending the dye into a chest that's right next to the ACT, rather than piping straight into the table. Nuclear Winter - is the chest an alchemical chest, or something else? ACTs can't pull items from alchemicals.

If you put a chest right next to the auto crafting table, it should grab the contents of the chest as needed to make the recipe, and keep the excess buckets in the chest until needed. Grab the items from the crafting table with a filter (maybe) or a wooden pipe powered by an engine, then send it on to where it's needed. Don't put an alchemical chest next to the ACT though, as they don't work with them.

Glass fiber cables will lose 1EU/t if the length is longer than 40 blocks, and wind mills have difficulty producing much more than that at the best of times, so if the cable from windmill to storage is longer than 40 you may be losing all the energy in transit. If this is the case, you could avoid the energy loss by interrupting the cables around halfway with a single batbox. What height are your mills at overall, rather than in relation to the ground? If they're lower than level 90, they won't produce much energy at all.

Oil can't be put into cells - it's from BuildCraft rather than IC2, so you'd be wanting to use the BC pump and send it through BC pipes into Tanks.