Ocarina of Time
Throughout the game, Link can obtain two upgrades in order to hold more Deku Seeds. One is found in the Lost Woods, where Link must successfully shoot the center of a target three times in a row. The watching Deku Scrub will then reward him with a Bullet Bag. The second upgrade is found in the Hyrule Castle Town Market. By shooting all of the rupees in the shooting gallery, a second Bullet Bag can be obtained. The order in which the bags are received does not matter. Each will increase the maximum seed capacity by ten, allowing Link to carry a maximum of 50 seeds.
Like in Ocarina of Time, seeds can be given as spoils when defeating certain enemies. In areas of the Faron Woods and Deep Woods, there are certain trees that when rolled into, will drop a shell containing Deku Seeds on the inside.
Cadence of Hyrule
In Cadence of Hyrule, Deku seeds are dropped by Deku Scrubs when defeated. They can be taken to Tingle in the Lost Woods, where he will eat them. In exchange for the first ten, Tingle doubles the heroes' stamina. Afterwards, the player can bring Tingle ten more seeds to unlock Yves as a playable character.
Deku Seed from Cadence of Hyrule