In this game, you need to give things to your research machine to unlock improvements. I was wondering, what items, in what tiers, are best to put into the research machines and what the value would be. Also, which items should you never use in a research machine?
The items you dig up from graves (other than amulets) seem to be purpose-built for researching -- they only require a shovel to acquire, and they give 80 research a piece. The only other use for them is to trade them for gold with the Pig King. Amulets, as of the Nov 27, 2012 update, provide resurrection upon death; amulets are probably too valuable to most players to exchange for research.
Tallbird eggs (cooked or uncooked) give 80 research as well, but fried tallbird eggs are a great food source -- if you have plenty of food and just want research points, this is a good option (and a better option than researching a bunch of other food to save the egg). Similarly, mandrakes give 100 research (also cooked or uncooked). These are quite rare. You can cook the mandrake to get the day-skipping effect and then use it to fuel research afterwards. Again, the sacrifice here is the very good food item, but if you have loads of food anyway, this isn't a terrible option.
Torches are a good renewable source of research points -- as far as I know, all crafted tools in the basic tier give 10 research points at 100% durability. Torches can be created with just straw and twigs, compared to the other tools which require you to use some of your flint (which is not a renewable resource).
Rope is a decent choice if all you have is grass, but torches are more efficient if you also have twigs.
If you have food to spare, cooked food gives more points than raw equivalents. Cooked monster meat is the first food I would sacrifice, at 7 points a piece, due to the negative effects of monster meat.
A (partial) list of items with research point values can be found on the wikia, although this doesn't indicate the worth of items in other aspects of the game.
To address the portion of the question about things you should never throw into the machine, I'd say never throw in any stone or flint (or anything created with stone or flint) because stone and flint aren't renewable in any way.
The diggable plants that you can harvest aren't renewable (although the resources you gather off of them are). Berry bushes (and possibly reeds) might be few enough and valuable enough that you wouldn't want to destroy them. Grass plants and saplings aren't renewable, but are common enough it wouldn't hurt to toss quite a few of them into the machine.
The Arqade question on renewable resources is a good place to start when trying to figure out what you should hoard rather than use for research.
At the moment the most efficient items I've found to fund the researches are the Grass Tufts and the Saplings. They can be found when digging cut or uncut Grass and both picked or unpicked Saplings with the Shovel. Each one of them gives you 20 research points, which makes them worth more than gold in this regards(gold nuggets only give you 15 research points).
It's still unclear if this is the intended behaviour and, being the game still in beta, it will be probably subject to change, but at the moment this is the most efficient way to fuel up your researches.
The best way to generate research that I've found is Rope, Planks and Torches. They are completely renewable, quick and easy to gather the resources for without danger, and provide a decent return. There are higher value materials available but these usually suffer from being rare, hard to acquire, non-renewable or have other important uses.