Sex

Sex was a process through which two or more individuals proceed through a process of sexual gratification.

The term 'sexually pair bonded' was used to describe a two beings in a sexual relationship in the 24th century. (NA: Shakedown)

Sex was also used to describe the gender of a particular species.

Incidents

The Doctor

The Doctor's sexual timeline is unclear. The existence of a grand-daughter, Susan, would suggest a coupling that produced one of Susan's parents; however, there are accounts (see Cartmel Masterplan) that call into question whether Gallifreyans reproduce sexually.
There is no chronicle that depicts the Doctor having sexual relations with any of his companions. However, Benny Summerfield and the Doctor's eighth incarnation apparently had a sexual encounter of some sort. (NA: The Dying Days) Although the initial chroncle left this open for debate, a later chronicle has Summerfield recalling the incident. (BFA: The Company of Friends)
In his ninth incarnation, the Doctor, utilizing a metaphor, indicated to Rose Tyler that he had "danced" before. (DW: The Doctor Dances) This metaphor carried over when his tenth incarnation entered into a brief but intense romance with Madame de Pompadour. (DW: The Girl in the Fireplace)
The most direct reference in the historical record to the Doctor having a sexual encounter suggests that the Doctor, during his tenth incarnation, had sexual relations with Elizabeth I during a brief marriage with her. It is known that she later developed a deep hatred for him, and that the Doctor suggested that her nickname "Good Queen Bess" was now invalid. Although his initial pronouncement to Ood Sigma could be passed off as humour, this account was later supported by future Queen Liz 10, and by the Dream Lord, who made comment of Elizabeth's other nickname, "The Virgin Queen". (DW: The Shakespeare Code, The End of Time, The Beast Below, Amy's Choice)
Amy Pond, following a near-death experience with the Weeping Angels and fearful of her upcoming wedding, attempted to intice the Doctor's eleventh incarnation into having sex with her, but he refused. (DW: Flesh and Stone) Later, after her wedding, she gives the Doctor permission to "kiss the bride" and later references herself and Rory having "a snog in the shrubbery", but in both cases the context was joking. (DW: The Big Bang)
An alternate version of the Ninth Doctor had sexual intercourse several times with his companion Emma, his next incarnation would later remark the that she was the only time travelling Companion he "had". (DW: The Curse of Fatal Death)

Others

Jan and Ace had rampant sex on Heaven. (NA: Love and War)
When Bernice Summerfield excavated Ice Warrior citadels on Mars she made love to a man called Tim in one of the egg chambers. (NA: Lucifer Rising)
The inhabitants of Delphon find the surgical removal of limbs to be highly sexually alluring. (NA: Lucifer Rising)
After getting to know (a clone of) Abslom Daak Ace considered having sex with him. (NA: Deceit)
Ace has sex with Bill Cook, first mate of the Arrow. (NA: Legacy)
Ace has sex with Thomas Dekker whilst in Chicago, 1929. (NA: Blood Harvest)
Roz Forrester decided in her youth that sex didn't offer anything that Martian Ale didn't. (NA: The Also People)
Chris Cwej had sex with a member of The People whilst at the Dyson Sphere. (NA: The Also People)
Jason Kane had sex with several aliens while stuck away from Earth. (NA: Death and Diplomacy)
Bernice Summerfield claimed to have had the best sex ever with Jason Kane. (NA: Death and Diplomacy)
Chris Cwej had sex with Ishtar Hutchings whilst on Earth in 2010. (NA: Happy Endings)
In the lead up to Benny's wedding, Ace has sex with a (clone of) Jason Kane. (NA: Happy Endings)
Ace lost her virginity to Sabalom Glitz on the floor of his spaceship. (NA: Happy Endings)
Chris Cwej had sex with David Daniels while on Earth in 1987. (NA: Damaged Goods)
Bernice Summerfield once accidentally had sex with a Citdbtbed. (BNA: Walking to Babylon)
Chris, after meeting with the Daleks, has sex with Christine Summerfield, just to feel something human again. (BNA: Dead Romance)
Khiste has sex with Christine Summerfield to prove a point about manipulation. (BNA: Dead Romance)
Bernice Summerfield's body has sex (whilst under control of Avril Fenman) with Adrian Wall. She fell pregnant with a half human-half Killoran baby. (BFBS: The Squire's Crystal)
In one timeline Samantha Jones lost her virginity at 15. (EDA: Alien Bodies)
Marie (a Type 103 TARDIS) was mated with a Type 105 on Simia KK98 to produce another TARDIS within her. (EDA: Alien Bodies)
Samantha Jones has at least two lovers whilst on Ha'olam. (EDA: Seeing I)
Fitz Kreiner has sex with Samantha Jones whilst in San Francisco. (EDA: Unnatural History)
Fitz Kreiner has non-committal sex within the structured reality of the Parallel stations. (EDA: Parallel 59)
Ace has sex with Kedin Ashar on Mendeb Three. (PDA: Independence Day)
Sarah Jane Smith has sex with Tom Ryder in China. (PDA: Bullet Time)
A gaseous species was freed from a meteorite that fed on sexual energies, killing several people in Cardiff in the process of its desire for these energies. (TW: Day One)
Gwen Cooper had sex with Owen Harper following a disturbing encounter with Torchwood. (TW: Countrycide)
Owen Harper had a brief sexual relationship with Diane Holmes who had fallen through the Cardiff rift. (TW: Out of Time)
Jack Harkness and Ianto Jones had sex on several occasions, in several areas of Torchwood 3. (TW: Adrift)
The Doovari's spacecraft were powered via a energy drive that was derived from the energy produced during sex. (WEB: Torchwood.co.uk)
Jack Harkness is known to have had sex with many different people and species.
Jack Harkness and John Hart allude to a sexual relationship when they re-meet one another in Cardiff. (TW: Kiss Kiss, Bang Bang)
In 1886 Clemency Eddison fell in love with a Vespiform who had taken the form of a human. She had sex with him and fell pregnant; the resulting child became Arnold Golightly. (DW: The Unicorn and the Wasp)
Around early 2006 a member of the Slitheen family disguised as Oliver Charles enjoyed a number of sexual encounters with Oliver's wife, mistress and a young farmer.(DW: Aliens of London),Doctor Who: The Encyclopedia
Adam Smith had sex with Toshiko Sato. (TW: Adam)

Other contexts

Many Time Lords dream of being a different sex (gender). (NA: Human Nature)
In one possible timeline, Time Lords who commit suicide regenerate into a body of the opposite sex. (DWU: Exile)
Iris Wildthyme confided in Sam and the Doctor that regeneration is treated on Gallifrey the same way that sex is treated on Earth. (EDA: The Scarlet Empress)
Jason Kane wrote several xenopornographic novels including Nights of the Perfumed Tentacle based on his sexual encounters with various species. (BNA: Beige Planet Mars)