I believe there are only 5 items that are missable. The rest are plot-related and gained through progression of the story.
These five items are:
- Brush: after checking on Hans, the cleaning Monk will rush off to the next screen. Follow him and he'll rush off again, this time leaving behind his cleaning gear that includes this item. It's meant to be used to uncover a puzzle clue but is technically unnecessary.
- Candle: when using the contraption near the Monastery's entrance elevator, you'll have to make a candle for Hans using herbs. However, if you first make a candle without the herbs, you'll receive this standard candle.
- Newspaper: after returning to the fenced hut area belonging to Ivan and Igor to recruit the youkai companion, head into the hut where Igor was sitting last time you were here. There is a table containing this newspaper. Picking it up also unlocks the 'Memory from Aralbad' achievement.
- Reindeer antlers: after waking up in the Youkai village, these will be in a box to the right of your hut's entrance.
- Youkai Medallion: once arriving in Syberia, exit your ship to the right, up some ladders to a gear post and inspecting the guard's skeleton. After a short scene you can obtain their medallion. However, if you miss this one after finishing the game, you can still 'continue' your game and it'll load the save before the final puzzle - from here you can easily backtrack to this item.
The full check-list that I kept track of is as follows:
*** Spoiler - click to reveal ***
Romansburg:
- Small key, coins, Katals candy, Fish candy, Gate key, Empty can, Jerry can, Token, Shroud, Hans' Shroud, Gold/Silver/Black/Brown Birdcalls, Winter clothes.
Note: 'Katals candy' is also known as 'Sugar candy' in other versions of the game.
Monastery:
- Scroll, Stained Glass Mammoth, Brush, Brother Alexi's Book, Youkol relic, Shears, Herbs and Brambles, Box of matches, Candle, Herbal candle, Oranate key.
Post-Monastery Romansburg:
- Mechanical heart, Newspaper.
Snow fields and forest:
- Branches, Offering, Russian doll, Hatchet, The Fisherman's Guide, Fish Tank, Orange Salmon, Fishbone, Rope with plate, Oil dispenser, Plan of train, Gauze blanket, Ivory knife.
Note: If you don't obtain the Fishbone here, you'll get it within the Youkai village instead.
Youkai village:
- Reindeer antlers, leather strap, Slingshot, Prayer wheel, Youkol mask, Empty flash, Cork bung, Flask full of water, Dream fruit.
Hans' dream:
- Mammoth doll, Attic key.
Post-dream Youkai village:
- Voralberg key.
Note: If you didn't get the Fishbone earlier, you will find it here in the youkai den.
The ark and ice fields:
- Narwhal tusk, Ivory hook.
Syberia:
- Youkol medallion, Stone plate (5 of them), Syberia flower, Ivory key.
I recommend following a walkthrough if you're not familiar with the game, keeping your own personal eye out for the 5 missable items mentioned above.