group items by classification & puzzles can accept anything from the classification it requires. For example a large object that needs to be moved will require an object classified as a lever but that object could be a crowbar, a pipe or perhaps even a particularly impressive erection as long as you don't mind your knob scraping over concrete (I know it'd make me lose my erection, I'm more of a metal kind of guy)

most items belong to several classifications at once. 
A crowbar can belong to 'lever', 'brace' and 'bludgeon' so it could be used as a crowbar (it'd be counterintuitive not to), used to hold up something heavy or used as a blunt weapon. 
A knife can belong to 'light slicing' and 'stabbing' so it will function as a tool for cutting lightweight materials (but not concrete or steel, not EVEN a ginsu knife can do that!) as well as a weapon
Wire can belong to 'conductor', 'tie' & 'garotte' so it'll be useful for electrical work, tying stuff up or strangling folk (perhaps those you've just tied up & electrocuted)

It'll allow players to use items in multiple ways but potentially get themselves into trouble if they need a specific item classification later on. The design challenge will be ensuring that there'll always be a way to solve the puzzles regardless of what item type they have or have access to in the area so they can't get into a dead end situation of "Oh you didn't pick up that tiny rock that was only 1 pixel in size back at the second screen of the game that's instrumental to this final puzzle? Well you've failed you IDIOT!" (AKA: the sierra dilemma) but still making the game a challenge to the player's puzzle solving skills. 

Items shouldn't be consumed unless they logically should be, for example a knife cutting cloth wouldn't be destroyed but a set of chemicals used as an improvised explosive obviously would be. 

Items can be retrieved when used in conditions like bracing or conducting but it will reset the state of the objects they were used on unless they've taken other actions to prevent that. For example if the player braces a door open so they can crawl through and then finds out they can jam the mechanism so the door can't move, removing the brace will leave the door open and allow them to reclaim the item. A wire used as a conductor to bypass an electrical hazard would be able to be safely retrieved if the player turns the power off since the hazard would not be reinstated and the wire itself wouldn't be conducting a charge. 

When items are used for improvised solutions, that's when they can risk being damaged or wasted. A pipe used as an improvised lever may well bend and not work for example, both failing the puzzle and destroying the item but pipes are common enough that it wouldn't break the game.

Restrict inventory size to a realistic amount but make items fairly common. Allow inventory expansion by finding backpacks rather than a guybrush threepwood coat where every pocket leads to a pocket dimension of infinite storage