Origin: Daniel and Charlotte presumably became friends after being recruited by Abaddon to find the island.
Since Then: After parachuting onto the island, they were separated. Sayid harnessed a deal with Locke to trade Miles for Charlotte, which reunited her with Daniel. Upon imminent rescue, Charlotte decided to stay on the island, telling Daniel cryptically that she was still looking for the place where she was born. Once the island moved and the castaways started flashing through the various time periods, Charlotte started experiencing nosebleeds. When they got themselves captured by The Others, Daniel professed his love for Charlotte to Richard. The flashes caused Charlotte's condition to worsen, and she soon died, but not before revealing that she may have met Daniel when she was a young girl living on the island. During the three years he spent on the seventies, Daniel tried to avoid her, but he finally talked to a younger version of Charlotte in 1977, thinking his plan to prevent the Swan Incident would work.
Origin: The two met several times over the course of their lives and afterwards, but each time, at least one did not recognize the other.
Since Then: Desmond's first contact with Daniel happened after his mind traveled from 1996 to 2004. He spoke to Daniel over a phone, and his mind then traveled back to 1996, leading to the pair's first chronological meeting. Desmond gave Daniel instructions that he'd heard from the scientist himself in 2004, helping Faraday perfect his machine for sending minds through time. Daniel then advised Desmond about the concept of constants, saving the man from death by temporal displacement.
Desmond forgot the experience, and he ended up on the Island, where he was shocked one day to find Daniel knocking on the door of the Swan. This time, Daniel was the one time traveling, and he soon vanished. Desmond showed no recollection of this meeting for years to come, and when Daniel came to the island in December of 2004, the two met as strangers. Daniel himself had forgotten their 1996 meeting due to brain damage.
Faraday guided Desmond by phone when the man became mentally unstuck in time, and he later discovered to his surprise a note in his journal about Desmond's importance. When Daniel himself became physically unstuck in time, he sought Desmond's help, leading to their meeting at the Swan.
Desmond finally recalled this encounter in 2007, and he followed Daniel's instruction to seek out the man's mother. He learned, in the process, details of Daniel's questionable experiments. The mission ultimately sent him into Charles Widmore's hands and back to the Island.
After death, the two met, and Daniel advised Desmond, sending him towards Penny. The two spoke of a common bond they knew nothing about while alive: Penny, Desmond's eventual wife, was Daniel's half-sister.
Origin: Daniel entered Eloise's camp, demanding to see the island's hydrogen bomb. She took him there, and he vanished.
Since Then: Decades later, Daniel entered the camp again, and Eloise shot him. He revealed he was her son before dying, and his journal confirmed his words. Eloise, pregnant with Daniel at the time, later gave birth to him off the island. Understanding his future and determined to keep him on his path, Eloise consistently pushed her son to succeed at mathematics, dissuading him from pursuing music. Her encouragement worked. Years later, she sent him to the island to his death. In the flash sideways, however, she postponed moving on so they could spend more time together.
Since Then: The brother and sister grew up without knowing each other. Penny also didn't know Eloise, Daniel's mother. In 1996 though, Daniel encouraged Desmond to speak with Penny to anchor himself in time, and his advice helped the two make contact again in 2004. Penny first heard of Daniel through Desmond, and she accompanied Desmond to England in 2007 when he searched for Daniel's mother.
The two never met while alive. After death though, they knew each other, and Daniel correctly refered to her as his half-sister.
Since Then: Daniel's mother never told him that Widmore was his father. Widmore followed his son's progress nonetheless, and he offered him a research grant when he graduated from Oxford. Years later, once Daniel's experiments had damaged his brain, Widmore offered to send him to the island to heal. Like Eloise, Widmore sent him to the island knowing he would die.