Well, I would want all puzzles to be obvious to a point. You gave a good example. Some games like to throw stuff in there that no person in their right mind would try to do.

If something like that is needed, then have an NPC that will give you that hint, or sell it to you for a price.

I want an average person to be able to figure it out, but I also want them to have to think pretty hard about it.

I haven't read this entire thread, but the primary thing to keep in mind is that a lot of the fun in adventure games is finding out what to use with what.

Anything where the answer to that is blatantly obvious should be automatic, everything else shouldn't be.

If you have to go with one system entirely, I'd stick with the more robust albeit more time-consuming use-this-with-this setup.

Personally, the interfaces used in the older Sierra games worked fine for me. You had a collection of icons ("eye" = look, "hand" = get/touch, "mouth/quote" = talk...), inclusing an invnetory option which you could cycle through. In all honesty, I don't think you'll need more than a 2-part command. "verb-subject" and "object-subject" will probably fit all your needs. After all, do you really think you'll need "open door with key" and "use key on door" when they do the same thing? In most cases, just pairing either a basic action or inventory item with the on-screen subject should do the job.
Also, if you want a lot of similiar items, you might want to group them somehow. The best example being the keyring.
Take a look at the older adventure game sytems, like AGS. They did a pretty good job of it.

I'd go for both options: manual and automation.

The first time the user encounters something, let him go through the manual process. Then if (s)he has succesfully navigated the 'puzzle' (puzzle meant in a very broad sense) and comes back to it later, have both options popup: the default action taken last time, or the expansive try anything option (this would map nicely to left and right mouse button).

The point being that the player does have to think which key to use, but once the key is used to succesfully open the door, the user shouldn't be made to search that key in the inventory again. You can choose to apply this to a single object, or all similar objects (in the case of the door I would apply it to all similar doors as well).

If the game is to be an RTS or action game, let me make a recommendation: gestures or radial menus, if you plan to use menus. WarWind used linear context menus for all non-default actions (like Windows does) - and its painful to use in a real-time environment. Radial or gesture-based actions allow you to memorise hand motions to perform common actions.

I replayed Beneath a Steel Sky recently and enjoyed their system. Right clicking examined an item and left click used it. If you moved the mouse to the top of the screen, the one row inventory would drop down where you could examine items, combine them or use them with on-screen items. Simple controls and full-screen gameplay.

It might seem limiting, but most of the time when I play point-and-click, it's blatantly obvious what you are trying to tell the interface to do and it's very frustrating hunting for the correct command combinations. For example, you use your security card with a card slot. You obviously want to open the door with it, not attack the door with it, push the door with it etc. You might even have to modify your environment to accomidate a simpler interface (for example, reduce the number of actions a single left click would mean on a specific object), but I prefer it as it's less frustrating and lets you get on with playing the game and solving puzzles.

Jiia, have one button do the automatic stuff and another for all the complicated indepth.

Feh, I say!

Make it automatic. Seriously. Hunting around in my inventory for the appropriate key or trial and error is tedious in the extreme. Don't put locks on doors that don't matter. If it's a simple locked door, like to a storage area, allow me to pick the lock in some way - and place a bonus behind that door for doing so. If it's a major door, maybe put a keycode lock on it.

Hunting for color-coded keycards is sooo Doom. It was annoying then (albeit made bearable by the fact that once you had the keycard, the door opened automatically once you approached it), it's annoying now. My time is precious; make every moment that I spend playing your game count, or it might be the last.

color key cards are out ... but not because the gameplay is bad, but because it is so OLD and so DONE ...

I mean it was basically the only puzzle that games on Atari 2600 had, go somewhere past some obstacle and collect some thing .... then go somewhere else to use it (although it was of course automatic in games that old, that couldn't have a real interface).

The real trick these days is not the interface ... picking items manually is fine ... IF you tackle the hard problems - IE creating puzzles and obstacles that are actually interesting and fun in the first place.

Like whoever played Bard's Tale or Wizardy I remembers that they we're so fun ... but 5 years later, that whole genre of games was getting tired and boring.

Good Luck to you.

Well, there's Gauntlet's approach: you have keys. Any key opens any door, but you have to find keys and each key only works once. Also, there are ways to open many doors at once without using keys, but that causes you to be surrounded by incoming monsters bursting from every door, so that's not a decision you make lightly.

Just give the players a good indication of how much mayhem is behind each door so they're not jumping into the void when they throw switch/open door.