Totally simple question: do you prefer to place system messages at the top, middle or bottom of the screen? Messages like 'You fell into a trap!', 'You acquire the Golden Shield!', 'Push the handle?'.

If at the top, then the choices window shows below it. If at the bottom, then the choices window shows above it. I'm used to placing system messages at the bottom, but then the choices window shows above it which might be odd and confusing: first reading the options, then the question.

I prefer to have dialogue at bottom, system messages at middle. Yet this will depend on the general UI you want to create. I don't think there'll ever be a definitive answer for your dilemma...

...but I'm positive options (choices) should always appear below the problem (question).

I'm not asking for a universal answer but personal preferences lol.

Yes, I agree options should appear below the question. Problem with having the system message at the middle would be blocking whatever is happening or has happened, though. 'You acquired the Golden Shield!' Great, but I can't actually see it right now and skipping the message will cause the character to tuck the golden shield in his inventory!

As for the UI, unless you're using a HUD (which I happen to be, but regardless), I don't see how much of a significance that has to one's preference of system message placement.

Well, you could always let the user select his preference. A few lines of script could handle that, right?

But no, I'm not a scripter, so I can't direct you to how to add that into your game - nonetheless, I still think this could be a valid approach.

I'ved always programmed them for all loctations, not just middle, top, and bottom. Also on the corners.

Not getting in the way of your scene, never doing that. Keep "item found" and "party joined" messages at mid top/bottom of the screen (not covering your character), also keep them low sized. Same goes for "x does y" messages in case sprites don't cut it. For speech, normal windows are fine but "bubbles" (like FF9 or Vagrant Story) look much better if you want a scene to look dynamic, and easy to decipher who is speaking now. (also, simultaneous messages) Use the former if you use huge character waist-and-up avatars, latter if you use small facesets or none. Just as using standard BS vs. custom BS, you get much better results if you use a script to draw the window. Both RGSS and eventing+patches allow relatively easy ways of coding your own, "advanced message positioning" script for setting exact location and size of the window, and of course drawing it yourself - as opposed to using a fixed size message window with just three possible locations.

Examples of perfect window positioning: Golden Sun (GBA), FF7-9/T(PSX), Chrono Cross(PSX)

It usually depends on the game. I like mostly putting my message boxes at the bottom because...well...I just like to! But, I do like games like FF9 & Chrono Cross where the messages are displayed in many different spaces -- so it usually just depends on the type of game.

Thinking of Kingdom Hearts, when you receive items, munny or exp it just appears in a list on the screen it dosen't just block anything behind it.