Blue Flower- I believe these are useless except as a hint that you have to go to Crock to get your missing character back (since Crock's hut is surrounded by vibrant, blue flowers).IUF tags- Not sure again, but I believe you can give these to Yamir if you didn't feel like going to Bayjin, and only wanted to deal with Nessie. Probably get less experience, since you don't come back with Glumph
Damaged Black Box- Only serves as a clue that you can use the HLL spaceport to analyze black boxes
Rotten Meat- You can combine it with Faerie Dust and put Bobo (the animal in the cage in the Trynton zoo) to sleep instead of fighting him
Bonecrusher Brew- Yep, just a drink
Powerpacks- Ammunition, I think they work on some W7 import items, although I think I heard that there is something in W8 that uses them?
Restricted Areas- You can never go into them easily. You can get into them without fighting however. What I do is enter fake combat mode and then run past the watchers. One of the restricted areas serves basically as just a connector between two areas of the bluff and is not essential at all. The other contains a decent weapon. This second area is a lot trickier, but I've been able to get into and get the goods many times without ever upsetting the T'Rang.
Umpani and T'Rang- They do not show up on Ascenion Peak. Some people speculate that the corpses you occasionally see are actually them. I like to think that originally they had been programmed to help you in the big ol' Rapax battle, but Sirtech cut that part out.
Hope this helps.