Update
Q: How do I know which version of the game I have?
A: Version 1.2 and onwards have the version number displayed on the title screen, but there's no clear visual distinction between the original release and Version 1.1. If you bought the game between June 8th and September 1st, 2014, you most likely have Version 1.1.
Instructions for application are included in the readme file you get with the patch.
Just in case, back up your save data and old "E1.rgssad" file before applying the patch (so you can restore it if something goes wrong). There shouldn't be any problems, but then again, you can see the notice at the top of every page on this site, so better safe than sorry!
Version 1.1
1. Eagle is a little more clear about the rocks that open secret passages in the Valley of Sol on Hobo Island.
2. Glymac mine carts made optional. Also moved treasure around to accommodate.
3. Vines in Elemental Shrine made optional. Significantly rearranged the end of the Elemental Shrine to accommodate, including the addition of two chests with Radiant Soma (at the end of each vine section).
4. Gatekeeper's Strength halved, no longer uses Cold Fear/Cripple, Poison Gas usage lessened.
5. For the last Agility trial in the Elemental Shrine, the exit was made an actual visible teleporter.
6. Crystal Eaters slowed, and you can now run from them (they just disappear until you enter the tunnel again). Also there's now a sign warning you of them.
7. Skull Pike and Ogre Axe from the shop in Endoria can now also be found in the caves you blow up in the Barren Pass.
8. When you offer the three relics of the zodiac at the Castle in the Sky, made it so you can't offer more than one Bow of Sagittarius, as the game would freeze.
9. Defense/Power/Mystic/Speed Rings from the randomly locked doors in Faust's House are now available in the Barren Pass bombable caves if you missed them.
10. You can no longer abuse the save & quit/Party Ball exploit to skip the battle with the Gatekeeper.
11. Added the following skills for Pica:
Sealed One: Comet Rain
Hellhound: Hell Tornado
Pied Reaper: Northern Lights
Antediluvian: Dragon Flare
Delila: Warped Affection
Astaroth 1: Star Cross (no longer causes HP degeneration)
Astaroth 2: Spectral Beam
Cugei: Chaos
Dark Saint: Icy Inferno
12. The golden humanoid statue enemy was given an actual humanoid sprite on the map.
13. You can still get Neo Tonics by trading in Spicy Herbs in Pepp even after getting the Black Diamond and not having taken Boaz there earlier in the game.
14. Astaroth now absorbs ALL Elements in Omni mode.
15. Added a chest with Radiant Soma on a previously empty balcony in the Elemental Shrine.
16. Fixed it so the Helper Chibi shows completion for Dimitri's ring/shard/crystal side quest in both scenarios (whether you brought him everything before Jessica faced her darkness in Cugei's Castle, or after). He also tells you where to find the rings in the post-game, if you haven't already completed this quest.
17. Fixed the Element Barrier chest in the Barren Pass cave (it gave you a Neo Tonic before, even though it said otherwise).
18. Exchanged the usage ratio of Troy's Body of Light with the weaker Rainbow Beam in the Gemstone Cavern battle.
19. Fixed sound effects for when you're ambushed by fishmen in Pepp Sewers (two of the touch events didn't play the additional "splash" sound effect).
20. Fixed an event that made Cugei look at you and play a sound effect in the Mirror Maze. In some cases, a sound would be played even if Cugei was no longer there.
21. Edited the dialogue when Cairo dies so Leonardo doesn't seem so callous about it.
22. Edited Leah's terror/shame/anger dialogue in Fiyara's inn (reworded it to be more personal and affecting, rather than just abstractly describing her emotions).
Version 1.2
1. Made it so "Granny's intro" event trigger is set whenever talking to her, so you can do the side quests with the other "grannies" even if you didn't talk to her before freeing Alavon.
2. Added a new event trigger for if you talked to Granny early in the game (before Glymac), that makes her recall her time with you when you cure her illness (this was previously the same as the "Granny's intro" trigger).
3. Removed an out-of-place window in one of the grannies' cabins.
4. Changed the Glymac university guard's mention of "education" to "knowledge".
5. Extended the duration of Dull Blades' attack reduction from 2 turns to 3 turns.
6. Extended the duration of Armor Erosion's defense reduction from the moment hit to 3 turns. Combined with the previous amendment, this should augment Esther's utility.
7. The second warp in the Reactor Core now upgrades the warp in the Elevator Complex to give you a choice of which floor to visit (B1 or B4).
8. Removed Icy Inferno from Saruma's repertoire.
9. Updated the title screen to display the version number.
Version 1.3
1. Fixed the Slimy Scale. Its inflicted condition now won't show up in your status, and it no longer poisons you (this was leftover from its previous effect).
2. Ben is now more susceptible to confusion (80% success rate instead of 60%).
3. The Hazel Omelette/Granny's Soup effects now last five turns instead of just one and two, respectively.
4. The final boss no longer uses Ungodly Rage and Strike Down.
5. Moved God's Hand to an earlier point on the Agility Path of the Elemental Shrine, so you don't have to pass any trials to reach it (you still need a Shrine Key, though).
6. The Celestial Coat, Chakra Wheel, and Mirror Vest from the Reactor Core can now also be found in the Elemental Shrine if you missed them. Relocated the booby-trapped chest with choking smoke to accommodate.
7. Increased the quantity of Radiant Soma in the chests at the ends of the vine-jumping challenges in the Elemental Shrine.
8. Changed the starry maze in the Elemental Shrine; instead of misleading warp pads, there are now treasure chests containing a Dragon Dress, a Dragon Tiara, Dragon Heels, and a Dragon Lash. These items could previously only be obtained as enemy drops.
9. An Aurora Sword can now be acquired after completing any of the three main paths in the Elemental Shrine. Previously, it could only be obtained as a drop.
10. A Brahma Weapon can now be found just before the Elemental Layout room at the end of the Elemental Shrine. Previously, it could only be obtained as a drop.
11. Many bosses up through the middle of the game (Maia is the last one) can now be made to flinch (40% chance), put to sleep, and paralyzed (20% chance each). Previously, these status effects could not be inflicted upon them at all.
12. The Wall of Death can't be confused or paralyzed anymore (not sure if there was anything that could do this in that situation anyway, but still).
13. Moved the Great Axe/Knight's Armor in Glymac Mines. They're now guarded by the Steel Dragon. Previously, they were at the end of the jump track, along with a Phoenix Feather, which is still there.
14. Maia's Flower Children can now be inflicted with a variety of status ailments (that battle really shouldn't have been as difficult as it was).