Is there any way (or anywhere) I can tell when it's OK to discard an Item?
I don't want to make the mistake of discarding a Quest Item, but my Inventory is beginning to fill up with things like Passports, Notes, and Matchbooks.
I have low CHA and can only have 1 follower.

There's no such a way.
You have to keep in your inventory anything that, hopefully, may become useful in the future, of find some safe place to store your items. Most of the containers will do. Except for trash bins - anything put in them will disappear after some time.

There are various locations where there are garbage containers on the street. Good if you just want to get rid of something, because the trash gets emptied from time to time. But there are non-trash containers in other areas (such as abandoned warehouses). If you're the Thieving type, I suppose you could try storing your stuff in a shopkeeper's back room, but if its his inventory container, it might end up disappearing because the shopkeeper sold it...not entirely sure on that, but since inventory changes from time to time, it seems a reasonable guess.

[edit] Ninja'd! And with less words, too!

Just, to give you a slight spoiler about two things you mentioned: The passport and matchbook are important (the matchbook moreso, if I recall correctly). I don't think you actually need them for the quest, but they do add some dialogue.

Generally notes aren't needed after you read them (unless of course you are taking a letter to someone for a quest) as long as you remember what they said. Things like safe combinations are needed in your inventory to open said safe, but after that is useless, for example.

SPOILERS

Blackroot and Dernholm is a smaller range. The cave is almost right in the middle between those two cities, if I remember correctly.

But yeah, good suggestion for a place to store stuff.

END SPOILERS