I've gathered about 12k worth of animal bits while riding around the Frontier, should I be holding on to (some) of them, or is it safe to sell the lot? Do the useful bits, if any, get sold with the rest of the junk if I choose to sell all?
The game also contains "shopping list" type quests, for which some hunting accouterments are required. Some of the hunting things (particularly cougar skins and claws) are hard to gather in a timely fashion, even with the hunter unlocked. You never need more than five of any item so every thing above that number is vendor trash. The homestead creation items are almost never worth the price in time and materials, even late in the game.
From the PlayStation blog post on hunting in AC3:
Game from the frontier offers a great many resources that residents of cities will pay handsomely for, so collecting the various pelts, meat and even bones or oils of beasts can be an excellent way to fund Assassins’ activities. There are also a few other uses for the bounty of the forest, but we’ll get into those in a future blog… we can’t reveal every secret just yet!
So there are other uses for animal bits. PlayStation doesn't want to reveal what they are yet. I, personally, haven't encountered any others in the game yet, but I'm fairly early on, so there are certainly things that I haven't figured out yet.
In addition to selling the items at peddlars, some of the items are used to craft other items at the Homestead. There really is no need to hold onto them however. Anything you may need to use for crafting can be gathered from the hunter on the Homestead, or you can easily catch more. I found the money was much more useful than holding onto the pelts.