Things I'd consider padding:
- Collect-a-thons where progress in the game suddenly stops until you go and collect X number of Y objects. Less egregious when the game lets you gather these collectibles at any time (Triforce Shards in TWW, Relics/Keys in Metroid Prime), not just once you reach the bottleneck where they're required (Tears of Light in TP and SS, Sky Letters in TP, pretty much all collectibles in SS). Items you get for beating a dungeon (Spiritual Stones/Medallions in OoT, Boss Masks in MM, etc.) don't count since these items are basically just progress markers for the dungeons themselves, which aren't padding.
This can also include items where quantities don't matter, but the game basically grinds to a halt at a certain point until you get them, and they aren't useful for anything but advancing the plot.
- Anytime that you're required to backtrack through an area, apart from returning to the area explicitly to access a portion of that area that was previously inaccessible. Having to go through an entire area again without the benefit of shortcuts also counts as padding even if it's to reach a new area.
Examples of pointless backtracking: second trip to Forsaken Fortress in TWW, second time facing Skull Kid in the Lost Woods in TP, going through Skyview Temple a second time in SS.
Examples of good backtracking: returning to Faron Woods to climb the Great Tree and access Lake Floria in SS, going to the Ice Cavern via Zora's Fountain in OoT, revisiting old areas in OoT as an adult (you can take advantage of shortcuts you discovered as a kid).
- Long strings of NPC-driven content that might have also made sense as a sidequest. If it could have been a sidequest, it doesn't need to bog down progress through the main content unless the player chooses to pursue it.
Examples: Everything that happens in the Ordon Village portion of the TP tutorial, up to the part where you head into Faron Woods. The game could have eliminated this segment entirely and given you access to the sword at any time of your choosing from the get go.
- Any time a minigame is required to complete the main quest of a game, unless the minigame explicitly serves as a method of traversal to a new area.
Example: Having to fly through Zora's River once was an interesting method of traversal to Zora's Domain. Having to fly through it a second time to collect Shadow Bugs was a pointless forced minigame.