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In 1998, 3 years after the original release, the first Suikoden was ported to the Sega Saturn, though not made by the same team it is considered a sort of Director's Cut version of Suikoden due to the game having some additional items and storylines. This guide will show you all known and verified differences.
Graphics

Due to the different hardware of the Saturn compared to the Playstation it appears they weren't able to reproduce some effects so there are some slight differences, others have had some enhancements and others appear to be completely pointless. The hardware limitations also effect loading times, giving the Saturn version about 5 seconds of loading when it changes screens, and they removed the "Now Loading" animations so it's just a black screen.

Black
Black Flying Towards Magician's Isle
Left: PSX - Right: Saturn
Appears to be a hardware limitation. Darn clouds.
Blue Chest
Blue Chests
Left: PSX - Right: Saturn
In the beginning of the game treasure chests are blue. Once you get to Toran Castle though, they're the usual brown.
Leknaat's Mosaic
Leknaat's Mosaic
Left: PSX - Right: Saturn
Leknaat's mosaic reflection on the floor is more defined and moved a bit.
Teleportation
Luc's Teleportation
Left: PSX - Right: Saturn
When Luc teleports you back to the beach the animation has changed to a lightning bolt. Hope that was a hardware limitation, cause that makes no sense.
Soul Eater
The Red Soul Eater
Left: PSX - Right: Saturn
The Soul Eater is substantially redder than it's Playstation counterpart.
Farewell
Farewell
Saturn image
When Teo says goodbye during the night it is no longer graytoned. That can't be a hardware limitation...
Blue Bandit Tea
Blue Bandit Tea
Saturn image
Ledon's "special" tea now turns you blue. Potent stuff.
Colorful Spin
Colorful Spin
Saturn image
The highlighter for selecting enemies and party members has been changed from it's gray incarnation and now spins in red, green and blue.

New items

Completely new items that are exclusive to the Saturn version. Note that both of these appear in Suikoden II.

Silver Armor
No image
1 of 2 possible prizes for finishing all 6 rounds of Eikei's Arena, the Silver Armor.
Stats: DEF +70 Auto-heal 20 HP

Darkness Rune
Darkness Rune
Saturn image
1 of 2 possible prizes for finishing all 6 rounds of Eikei's Arena, the Darkness rune, complete with one entirely new spell (for Suikoden that is).
LV 1. Finger of Death - Inflicts Instant Death / 1 enemy.
LV 2. Stealer of Souls - DMG / 1 enemy.
LV 3. Black Shadow - DMG / all enemies.
LV 4. Hades - Inflicts Instant Death / all enemies.

Mini-games

All the mini-games have been changed, from Chinchichorin to Marco's cup game. This is a list of who plays what.

Marco
Guess Heads or Tails for all 3 coins
Tai Ho / Gaspar
Guess the total sum of all 3 dice
Georges
A game of 21 / Black Jack

Eikei's Arena

Completely new addition to the game, Eikei has moved to the roof and opened an arena with some special prizes for the toughest fighters in the Liberation Army. The only place to get the Darkness rune and silver armor.

Arena Using his Lion's Trial Rune, Eikei will summon monsters for you to fight, giving a brand new battleground for you and your enemy to duke it out on. Pick your fighter and fight as long as you can, no healing will be granted between rounds or matches and instant death spells will be useless in this trial.

Fighters will need to possess both physical and magical prowess to succeed, clever use of a Mother Earth rune is highly recommended.
Eikei pulls no punches here, return the favor.

Fight Round 1: Eagle Man - Kobold (mage) - Strong Arm - Delf - Slot Man Prize: Crimson Cape
Round 2: Devil Shield - Death Machine (sword) - Mad Ivy - Grizzly Bear - Creeper Prize: Power Gloves or Rage Rune
Round 3: Nightmare - Sorcerer - Banshee - Demon Hound - Gigantes Prize: Master Robe
Round 4: Black Elemental - Demon Sorceror - Rabbit Bird - Hell Unicorn - Dragon Prize: Horned Helm
Round 5: Magic Shield - Clay Doll - Siren - Magus Prize: Windspun Armor
Round 6: Sunshine King - Zombie Dragon - Crystal Core Prize: Darkness Rune or Silver Armor
Prize
After completing a round you may choose to continue or claim a random prize for your rank.
Failure to complete a round will result in a total loss, you will not receive any prize for your progress.
E.g: falling in round 6 will not yield the prize for having completed round 5.

Story Events

The Saturn version has added two entirely new events and expanded greatly on an existing one.

New event: Pet Cat

Random event after beating Teo.

Kitty-cat
Cat
Text: You can raise the cat in Hero's room at Orange Castle.
Entering Kouan and approaching the boxes near Lepant's house, you may hear a cat meowing.
This event is random and there is no info given by anyone that it's available.
The cat has no sprite and is just sound.
Kitty-cat The cat takes residence among the boxes in the hero's room, still no sprite.
You can feed the cat, play with it or hit it to level it up.
Doesn't appear to actually have a function beyond this.
Kitty-cat If you get the cat before you have a level 4 castle it results in a weird bug where an elevator door appears in the hero's room...

New event: Pirate Attack

Random event after before recruiting pirates.

Pirate Attack
Pirate Attack
Upon returning to Toran castle Sanchez will inform you that something terrible has happened!
Pirate Attack The dastardly pirates have attacked and kidnapped two random girls from your army. There's only one thing to do: get them back.
Pirate Attack Amazingly enough, if Mina is kidnapped she'll prove that the dance she did during your recruitment of her wasn't a fluke and dances for her captors. Apparently she simply needs to be prodded with a slight case of kidnapping before she actually dances for anyone.
Pirate Attack A trip to the Pirate's lair and a quick fight later the girls are rescued from their captors.
Now you just have to go back home and get Tai Ho and Yam Ko and recruit the pirates to your cause. I sense some awkward dinner gatherings at Toran castle in the future...

There are nine girls that can be kidnapped in total: Lorelai, Meg, Valeria, Apple, Lotte, Onil, Sarah, Mina and Esmeralda. Each will have some unique lines of dialouge.

Expanded event: Gremio's Resurrection

Control Gremio as he wanders the afterlife looking for McDohl. A place where no one will speak to you and doors won't open, a bleak mirror of the real world

Gremio's Resurrection
Gremio's Resurrection
Upon gathering all 108 Stars of Destiny before the final battle
Leknaat: Soldiers of the Liberation Army, quiet your minds and remember your friend.
Scene change: Antei
Gremio: Where is this? I get the feeling I came here once with Young Master. Why am I here?
McDohl runs by
Gremio: Ah! Young master?!
Gremio: Where are you going? Wait for me.
Gremio's Resurrection Scene change: Seika
Huh? Isn't this Seika..? When did I..?
I remember now... when we came here, Young Master had trouble convincing Mathiu...
Anyway, I should look for Young Master.
Player controls Gremio, encounter McDohl at the lake
I've been looking for you, Young Master.
McDohl runs away
Young master! It's Gremio. Don't you remember me?
Gremio's Resurrection Scene change: Rebel Hideout
Gremio: This place... This is where Lady Odessa died...
I wonder what kind of person Young Master would have become if we hadn't happened to meet her back then..?
Scene change: Gregminster
Gremio: This is... a dear city...
A dear home with Cleo, Pahn, Young Master, and Master Teo.
I wonder if we can ever go back to that time again...
Scene change: McDohl house, kitchen
Gremio's Resurrection Gremio: Don't go anywhere now, it'll be ready soon.
We can start setting the table soon.
Scene change: McDohl house, dining hall
Gremio: Young Master! Ted! Dinner is ready!
Teo: Everyone, your attention please. Tomorrow morning, I must travel north.
Hero will be the master of the house while I'm gone. I want you all to give him your full support.
Teo: Gremio.
Gremio: Y, yes!
Gremio's Resurrection Teo: You've taken care of Hero since he was little.
Thanks to your efforts, he's grown into a fine young man. I'm grateful to you.
Gremio: No, I... This is my job...
Besides, it's my pleasure to serve young master...
Teo: Good. I hope you continue to watch over him.
Cleo, Pahn. I'm counting on you two as well to help and protect him.
Cleo: Yes, Lord Teo.
Pahn: Of course, sir. Leave it to us.
Gremio's Resurrection Teo: Ted. I hope you will always be a good friend to Hero.
Ted: I'd be Hero's friend no matter what you say. Right, Hero?
Teo: Enough talk. Let's eat before the food gets cold. Let's raise our glasses.
Teo: To my son and to the Empire.
Fade to black. Note: from here on it's the same as Playstation version
Gremio: Ah... I don't want to die in this kind of place, I still have much more to do for Young Master's sake...
Leknaat: Be opened, the gate of dimensions, connect the hearts of the 108 stars that are here, and that man to this place...
Scene change: Toran castle
Gremio: Come to think of it, there's still laundry to collect...and a new stew...