Here are some where the relationship is a secret, although not all of it is 'under the scoobies noses' type of thing. You'll have to decide whether any of them fit your pleasure.
His Dirty Little Secret by jamesgirl
Summary: William 'Spike' Giles and Buffy Summers are both students at Sunnydale High, but they lead two very different lives. Spike has it all – looks, wealth and popularity. Buffy has nothing – since her parents divorced, she's been living in the servants' quarters of the Giles mansion, where her mother earns a meager living as a maid. But beyond these differences, they have a secret relationship – at school, Spike pretends not to know her, but at night he visits her room with growing regularity...
King of Hearts By Charlie
Summary: AU/Fantasy. Inspired by "King Ralph". Spike is a rock singer at a London club when two men show up, telling him he is the rightful heir to the throne of England. A beautiful housemaid at Buckingham Palace catches his eye.
Oedipus Calling by Addie Logan
Summary: Buffy Summers is sure she's found Prince Charming in her new husband, Liam Angelus. However, when a surprise house guest changes everything, Buffy learns how quickly a dream can become a nightmare.
The Arrangement by jamesgirl
Summary: Five years after the tragic death of her husband, Angel, Buffy Connors (nee Summers) is the mistress of the powerful and sinfully sexy, William 'Spike' Giles. But their red-hot liaisons are nothing but a way of fulfilling their natural sexual needs. Spike needs a woman in his bed, but has an anathema for committed relationships, and after losing the love of her life, Buffy's not looking for any kind of long-term involvement. The arrangement they have works for both of them as neither have any desire to fall in love. So when their feelings start to change, they both cut and run...
The Education of Buffy Summers by SeaBlue
Summary: Bad girl Buffy Summers is shipped off to boarding school...where William Bloodsworth will give her a more thorough education than she ever dreamed possible.
A Glimpse Into An Affair by tahmoe
Summary: Elizabeth and William are two strangers who walk into a coffee house but walk out as something different. | 
