Well, here goes. I decided not to format it like the Greninja combo thread since so many of Links combos work differently on different characters and for simplicity. For the true combos, I'm testing these on training mode Mario and seeing if the combo meter registers them as combos (though some true combos are not registered for some reason). Most fast fallers and big characters are susceptible to most of these combos at higher percents than listed.
Blue means the combo is a true combo at most percents and cannot be escaped by the opponent once the initial hit is landed.
Green means the combo is almost guaranteed, but can be interrupted by the opponent. Some can be true combos at certain percents, but the window is much smaller than blue combos.
Yellow denotes combos that rely on reads and none are guaranteed. You need to anticipate an opponent's behavior (such as airdodging, shielding, jabbing, throwing out an aerial) to make these work.
Bomb throw > almost any attack (% damage varies)
Let's get the most obvious and important one out of the way. Most Link mains should know that a bomb throw leads into lots of attacks. The explosion has a lot of hitstun and Link does not get hurt by the explosion if it hit the opponent. The bomb sends opponents at a 70 degree angle away from the side they got hit by the bomb. First of all, there are many way to throw the bomb to initiate this combo. JCT and Bombsliding are good options when grounded. However, bomb combos also work in the air. For example, you can down throw a bomb and footstool the opponent while they're in hitstun from the bomb. You can also up throw a bomb into an upair. If you can catch someone off guard near the ledge, you can actually JCT a bomb at them and immediately follow up with a Dair spike, but this is extremely difficult to land.
It's tough to be more specific with this because of the many combo possibilities, but bomb combos are definitely something you need to learn. Although your follow ups change based on how much damage the opponent has, you should most likely be able to chain something if you threw the bomb close enough to them and you're quick enough. Although you can of course try your own bomb combos, I recommend the following:
Forward throw > Fsmash - Does the most damage out of any two attack bomb combo (25%), but only works at low percents.
Forward throw > Ftilt - This starts to be the more reliable option once the opponent is at mid percents.
Forward throw > Fair - At some point, the bomb will still knock them high enough that Ftilt will no longer reach them. Fair one is a good option at this point, but you can also try to Uair if you notice the opponent is DIing back towards you.
Down throw > Nair - A good anti-juggle option if you happen to have a bomb in your hand or if you want to approach from above. If you have good timing, you can try to dthrow > Dair, but it is risky if the initial down throw missed.
Dtilt > Fair (18% if only Fair 1 hits, 30% if both Fair 1 and Fair 2 hit)
After landing a Dtilt, immediately fullhop and Fair. You have to be very quick with this, otherwise the opponent can escape after the Dtilt. You are most likely going to only get Fair 1 as a follow up, but a very low percents, you can land Fair 2 as well. This is a true combo until around 30%. Very solid combo, better used near the ledge for a possible edgeguarding opportunity.
Dtilt > Uair (27%)
After landing a Dtilt, immediately short hop or full hop depending the opponent's % and Uair. Again, need to be very quick with this otherwise the opponent can escape. This is a true combo until around 69%. In most cases, this combo is superior to Dtilt > Fair because of the damage, large % window, and juggle opportunity. Dtilt > Fair might be better when used near the ledge on character with bad recovery option, but obviously very situational.
Sourspot Dair > Dair Bounce > Uair (23% or 38% with Uair)
Very hard to land combo and only works at low %, but it is a true combo if hit correctly. A lot of you may have "accidentally" done the first part of the combo, which is essentially using the sourspot Dair (which only appears after the Dair spike and the strong hit Dair hitboxes go away) to bounce into another dair following their hitstun direction (if you fast fall, you don't bounce), which ultimately leads to an Uair.
This combo is weird in that it actually works better on floaties. Fast fallers tend to be able to escape the bounced Dair. Big characters are especially vulnerable to this. It is a 3 hit true combo on Mario around 20%. Uair can sometimes be missed, but for the most part it is a reliable finisher.
Other combos I need to test further:
Bair (1) > stuff
Jab > stuff
Boomerang > Fair
Zair > stuff
FF Nair > stuff
Uthrow > Utilt on fast fallers
Utilt > Uair
Dthrow > stuff
I'll probably slowly add stuff to this, so continually check back on this post. If you guys have any suggestions/contributions, feel free to share. I think later on I'll expand testing these combos to characters of other extremes like Jigglypuff, Fox, and Bowser to get more accurate % windows on the true combos but for now I want to focus on getting a list done.