Spike and Angel (in text: "Angel and I were never intimate, apart from that one time.") Joss Whedon has also stated that Angel and Spike have had at least one sexual encounter, which technically makes this one canon. Ironically, in the Dark Horse Presents online special "Always Darkest", Buffy has a Spangel nightmare.
Angelus: Do you have any idea what it's like, having nothing but women as traveling companions, night in and night out? Don't mistake me. I do love the ladies. It's just lately... I've been wondering what it'd be like to share the slaughter of innocents with another man. Don't think that makes me some kind of a... deviant, hmm?
Wesley and Gunn
Pretty much all of the Thin Dead Line.
Angel and Lindsey (note that this became text: Darla's "It's not me you want to screw. It's him." and Angel's "I want you, Lindsey. Thinking aboutrephrasing that." - tenuous text is text all the same.)
Let's not forget Lindsey wanting to know EVERY detail about the Darla's *ahem* encounter with Angel in Epiphany. ("You want details Lindsey? Is that want you want?" "Yes I want details. I need to know everything, all of it. What did he do to you?")
Angel and Wesley. This even extends to Angelus, who brings it up when mocking the Gunn-Fred-Wesley triangle ("He's damn near perfect; if I swung that way..." He then goes on to describe Wesley's ruggedly handsome features, his fetching accent...Thank you, Joss Whedon.)
There's also the conversation between the old man who took over Angel's body and Wesley in "Carpe Nocturn."
Angel and Doyle in early Season One. ("Maybe I'm a little attracted.")
In the episode "Birthday" it is said that Doyle could only pass on his vision ability to Cordelia because he had romantic feelings for her. Later in the same episode it is revealed that Doyle passed his visions to Angel in an alternate reality, which implies that he had similar feelings for Angel (at least in this reality).
Spike and Gunn ("20 minutes from now he'll be popping up next to you in the shower, making cracks about your... am I the only one he does that to?")
Darla and Drusilla. In text, they once had a threesome with The Immortal. And in flashbacks, it is implied that they would retreat to each other's...company when tired of Angel and Spike. And a bath together afterward ("Will you hold my head under the water?").
Their first conversation after Darla is re-sired is referred to as a make-out session by one unfortunate human witness who also calls them girlfriends. Drusilla calls Darla 'my sweet', which is something she and Spike used to call each other when they were lovers
All of which is made creepier by the fact that Drusilla has a tendency to call Darla "Grandmother".
Lampshaded by Gunn the episode after Darla's re-siring. After having the whole vampiric 'family tree' explained to him, he mentions that 'the granddaughter re-making the grandmother' weirds him out more than everything else.
Lilah and Drusilla. The sensual way Drusilla strokes her face in Holland Manners house
Lilah and Faith. Lilah picks up Faith at a club in order to recruit her to kill Angel. ("I think you misread my intentions")
Lilah and Fred. Lilah had a habit of getting a little too descriptive for this troper's tastes.
Lilah and Cordelia. ("Are you trying to turn me on?")
Lilah and Bethany.
Fred and Cordy have their moments.
Fred and Willow in the latter's season four guest appearance has spawned a slew of femslash from a few minutes of shared screen time. ("I'm seeing someone")
Hilariously, Wesley looked kind of freaked when they met. With his onscreen love interest and off screen fiancee instantly getting on so well and having so much chemistry, no wonder.
The whole episode "Disharmony" one ooey-gooey bucket of Harmony/Cordelia Les Yay. "The last time I remember being happy was with you." And don't even get started on the Mistaken for Gay sequence.
Pavayne and Spike, in the episode Hell Bound, is primeNo Yay.
Every time Andrew appears on screen, his reaction to seeing Spike reaches the highest levels of Ho Yay, much to Spike's annoyance.