I am having an issue, I am having a problem. I'm afraid my mind isn't mentally capable of plotting out difficult puzzles. I need to have lots of puzzles in my game, but the issue is I can't think of anything unique. :S Not only that, but I don't even know if I can event difficult puzzles without major complications. I am pro at making cinematic events in RPG Maker VX, but the thing is... I suck when it comes to crazy variables and custom scripts. If ANYONE knows any ideas they can give me, and maybe even how to event them while I have moderate knowledge of eventing, PLEASE give your two cents on this.

I'm guessing that you need the puzzles for obstacles in dungeons? There are many kinds of puzzles that can be used, but it seems best to have puzzles that make sense in context. For example, you're not going to have a hardcore lava rerouting puzzle in a poofy bubblegum cloud dungeon that's a bazillion feet above sea level.
Give us a short summery of what type of dungeons (what theme, what climate, what types of creatures inhabit the interior and exterior, etc...) you need puzzles so that others like myself will be able to assist you.

Alright, how about this: A natural underground cave (think of it of a more sandy underground cave) and it may crumble at anytime. There's a nice setting for you.

You could have a quicksand puzzle, player has to learn which tiles are the quicksand and know how to avoid them, and if they wander too close have to mash the action button in order to get themselves out or be sucked in and game over.

Or you could have different 'levels' to your dungeon, and certain paths are only reachable by climbing vines, essentially making the place a maze and the player has to figure out which path to take - this also opens up the "I can see it, but can't get to it!" type of puzzle. Like say you put a treasure chest on a map, and they're only a few tiles away but there's something blocking their path and they have to figure out how to get to it.

If there's water in this natural cave, you could have a dam and water control/re-routing puzzle - think FF9. Different switches change the path of the water, enabling them to reach other areas and blocking off others. Or a waterfall re-route puzzle.

Well thought dungeons usually provide hints as to the dangers within and usually are a mini pre-cursor to the inevitable boss.

I have more ideas, but that's all I've got at the moment.

Don't forget the blocked cave entrances "how do you move that block", or puzzles with the mining carts - using switches to get them in a certain position.

Caves full of bats and one drops a certain item when you kill him.

I love puzzles.

Two things to keep in mind when building a puzzle:

First - A prize. Puzzles should typically lead to a prize. Usually an item but this is an area in which you can be creative in what the player gets. Prizes are the only reason players do puzzles in games.

Second - However if the puzzle is main story progression, you ALWAYS want the puzzle to be engaging and capable of breaking the monotony. Puzzles can even occur in battles, or you can turn a battle style into a puzzle that will take place in the main story from time to time. (Suikoden is an example.)

Thus, know why you're building a puzzle. Some puzzles hybrid these two things, in which case you'll want to use the second with an optional completion in mind that makes the initial challenge greater.

Battles that have nothing to do with the story progression can and should be challenging. The greater the challenge, the better the prize.

Once you've done this and figured out if a puzzle is necessary and why you're doing it (You want to make the game more fun and break monotony, which may include the addition of a prize) you'll want to grab a piece of paper and a writing utensil.

There's a number of puzzles. Switch doors, push boxes, timed progression, timed switches, increase and decrease switches, catching objects, herding objects, visual or audible ques, dodging objects, mazes. It's all about using the game mechanics to your advantage.

I'd suggest using mazes in your underground cave as well as events or puzzles that if done incorrectly will cause the ceiling to become more and more unstable. Once it reaches a certain instability, the cave collapses and it's game over. You can even put optional puzzles that lead to prizes but cause great instability, thus making them riskier to attempt.

Personally I find that a very good way to keep puzzles from becoming stale as the game goes on is to include tools, like Zelda/Wild ARMs/Lufia 2. Giving the player a hookshot or bombs or a lantern is a good way to keep them interested in the puzzles and to provide a sense of escalation as the game goes on.

Here's a really good article deconstructing how puzzles are handled in Ocarina of Time. It's a solid read if you're planning on including puzzles of any type, and especially if you want to use tools.

I don't really have any general advice for making "challenging puzzles." I generally have the opposite problem. My puzzles are so hard that people think they're bugs. Especially my riddles. But... even some of my block puzzles have that problem. I guess my advice would be to play (or watch videos of) Lufia 2, Wild ARMs 1 through 3, and some of the Zelda games. These are games that are famous for their focus on good puzzles in dungeons.

I'm not great at puzzle design, but essentially the mechanics work like this: Simple puzzles will need only a couple of switches or variables. Advanced complexed puzzles will probably need a lot of switches or variables or both. You mentioned that you aren't very proficient with variables, so that would be the first place I'd go.

Regardless of the engine you are using, there are a lot of tutorials available that teach the use of variables. If you learn it in one engine, you should be able to use it regardless of any maker you use.

Here is a link to a tutorial for variables using the RMXP

http://www.rmxp.tigerseye.uk.com/tutorial_event3.shtml