Is there a tool that can tell you what alchemy ingredients combine into that takes into account the mods you have installed? Similer to http://www.uesp.net/morrow/hints/potion/PotionHelper.shtml but like I said, takes into account the mods you have installed.

Such would be quite impossible. Even with MWSE there is no way to determine what effects an ingredient has.

I won't say it's impossible. I don't mean an in game tool, I mean something outside the game. I mean, even the CS of course can tell what effects an item has. There is such a tool for Oblivion. I just haven't found anything similar for morrowind.

That would be quite different but as of yet there is no such tool. It should be easy enough to read the load order and scan for only the ingredient records. You might try posting a message on john.moonsugars's tes3cmd thread or PM'ing him.

It wouldn't be too hard to write a tool to output a report that would show you all the ingredients for a given effect. http://code.google.com/p/mlox/wiki/Tes3cmd doesn't quite do this in the most usable way, but you could try:

tes3cmd dump -l -t ingr -m invisibility *.esm *.esp

and that would list the ingredients that match "invisibility". It doesn't take into account load order though.

Interesting. I may try to make something like this. With the help of tes3cmd it may even be possible.