LIGHTNINGLORD2'S PROFILE

I mentioned this approach in an article already: You can easily balance stats via doubling approach. Enemy is too frail at 50 HP? Set it to 100. Still too frail? Go for 200. Too much health now? Roll to the middle of 100 and 200, which is 150. Assuming this is still too high, you can go to 125. Doubling/halving a stat is always going to be significant and gives you a range in which the stat is balanced.

Ways you can avoid inability to deal damage:
-Dragon Quest gives you a 50% chance to deal 1 damage if you wouldn't be able to damage the target. I think one of the RPG Makers has this as well. In DQ, this is only really relevant for hitting Metal Slimes (the basic version has 2 HP and 255 Defense).
-Dragon Quest also has a command to charge up an attack - if you spend four turns charging, the power of your attack will be increased tenfold.
-A division-based damage formula such as a.atk^2/b.def
-Skills whose damage calculation does not include the target's defense
-Slip damage states
-Disgaea has you assign attacks first, which you have to execute via a menu command all at once. Letting multiple people gang up on someone gradually boosts your damage output, which is crucial in damaging obscenely overlevelled enemies.
-Don't have a defense stat at all
-Instant death skills

There's a few that I enjoy, which are mainly Pokémon ones:

Ice Path from Pokémon Gold&Silver is one of my favourite dungeons of all. Not only does it have a nice background theme (shared with Dark Cave and Whirl Islands), the lack of trainers gives the path an overall relaxed theme. Though there is a few NPCs in it in the remakes, those are temporary and mostly unobstrusive. Furthermore, the BGM was remastered in a great way.

Another good one is the Distortion World in Platinum. A mysterious, puzzle-oriented dungeon with a good amount of exposition and great focus on the only two fights (vs. Cyrus and vs. Giratina). Not to mention how this dungeon is introduced.

From Black&White, we have Chargestone Cave. This is proof that it's possible for a dungeon to be original. It also has some cool Pokémon, some interesting story encounters (such as the first meeting with the Shadow Triad) and decent puzzle elements.

Sky Pillar from Emerald wasn't all that interesting, as the puzzle is annoying and all you do is watching Rayquaza fly off at the top. Omega Ruby&Alpha Sapphire make it far more exciting as the final dungeon of the Delta Episode, giving it an amazing design and has you catch Rayquaza by bringing seven Dragonballs Key Stones. Rest is spoilers:

author=oddRABBIT
You were a bit late to that answer, FlyingJester. pianotm already answered.

EDIT: Here's a puzzle.

I have three special four-sided dice. They have one letter on each side. When I roll them together I get three random letters which I try to rearrange into a word. In my eight goes so far I have made the words:

CAT, SON, POD, RIG, PEG, TAP, DIN, APE

What are the letters on each die?

Solution:

Final Fantasy also tries to come up with a unique system about how you're able to improve your characters aside from just leveling up (which often is a very minor aspect in itself in later titles).

RPG Maker 2003 uses an ATB System by default - so it would be easier to style it after FF4-6 (which use a similar graphic style and the early ATB system - in fact, several parts of the RTP are sprite rips from those games and a few other SNES RPGs)

Summing up the five posts above, everyone has his own way of balancing stats, be it with brute forcing, guesstimating, calculating, spreadsheeting... the possibilities are vast.

If you ask me, in a good RPG, the skills your character has available are more important than the stats.