I have a Timer feature which was a relic of an original (as in, one of the first concepts, not that there's nothing else like it) game concept I had. Well... 9 timers. They sort of do the same thing, but I go back and forth about putting them on the "chopping block".
Basically, I have these items that are detrimental to the characters (they have issues that can be overcome) and I want the player to make the decision to have these items equipped as often as possible. The concept was that to execute this, I'd simply use a timer and not tell the player about it, so that they wouldn't exploit it (Example: Waiting around and doing nothing). This timer would tick to a set amount of time (something like 2 hours of real time) and then the item would "transform" into something very beneficial.
Bad concept for about a hundred reasons. The reason it remains currently in my game is simply as an "alternative" to the way these items currently work. The items themselves now need to get a variable to a specific number before the "transforming" happens. This variable goes up for having the item equipped during certain battles (usually boss encounters... the Troop Pages have a check in there at the beginning of each combat to see if the item is equipped. If so, it raises the variable by a set amount and then flips to turn off the check so it isn't made constantly) and during certain conversations. For the conversations, it checks if the item is equipped. If so, your "choices" are different and one of them is linked directly to raising this variable. The meter I'd decided on was something like 250 total points needed. The timer itself... after it runs down a custom invisible timer of 5 minutes... adds 1 to the variable (conversations add 5-10 depending on significance of the dialogue) and the battles add 10-20 depending on difficulty.
Now, I'm not sure I'll keep that timer as having 9 of them going at once can cause lag in some areas of the game, but I do also like having it for the purposes of "getting around" difficult fights or "not finding the right conversations to use it". I've also thought about going back to a "on screen" timer for this instead of having a ton of variable timers and just having it be "universal" so long as any of these 9 items is equipped... and then simply raising the variables of all of them by 1 once the timer hit's 0 and start again.
I did once tinker with a puzzle that required you complete it in 3 minutes (push boxes onto switches, timer went down during combat as well). But, in general, it promoted this "rush" mentality that just didn't work for puzzle solving. I'm sort of one of those people that is like, "if you want me to rush, I'll rush, but if you want me to solve a puzzle, you can't rush me. Give me time to do the puzzle or remove the puzzle so I can rush". I just didn't find the concept fun, so I scrapped it.