Ziva's first appearances in NCIS aren't strictly speaking ho yay - at least not with another character. It might just be to give Tony nosebleeds, but... I've never seen someone actively attempt to imply that they're bisexual, if not an outright lesbian, who actually isn't. It never develops into much later on, but... really. Naturally, these traits carry over to her sadistic, villainous sibling as well, though that's vaguely fanonical.
Ziva didn't have tension with another character when she first appeared? They spend an awful lot of time on her close relationship with Director Shepard, after having her first onscreen conversation mention lesbians. More recently, in the season 6 episode "Caged", Tony starts the episode discussing his plans to ask out an attractive female coworker, only to have Ziva inform him that "Hannah" has asked her out to lunch. Twice. When Tony asks if she accepted, she smiles and doesn't reply.
In one episode, Ziva told a suspect flirting with her that he wasn't her type. The guy was, for lack of a better word, a smuck and was obviously not someone a straight Ziva would go out with. However, if someone was looking for clues Ziva was gay, that wouldn't be bad evidence if used with subtext.
There was also some flirting between Abby and Kate in the early episodes.
Abby: Admit it. You just like strappin' on a gun.
Kate: More than one.
Abby: Really? You packin' more heat than meets the eye?
Kate: Those your only tattoos?
Abby: You show me yours and I'll show you mine.
Also in "Doppelganger" when Kate is annoyed that she's been left to handle the phones.
Kate: Hey, what is this... boys night out?
Abby: Which means Girls Night In. Transfer your phones to my lab. (Kate smiles and does so, then the two walk off hand in hand)
There are plenty of Youtube videos that hint at a relationship between Abby and Ziva. Some of the clips in these videos are pretty convincing.
Or it could be that Tony is mature, reasonable, and intensely loyal to Gibbs - as Gibbs makes perfectly clear when he suggests to Director Shepard, without any prompting whatsoever, that it's time for Tony to have his own team. And he sounds truly regretful about it. Of course, Tony has absolutely no intention of leaving Team Gibbs. Under any circumstances. Not, of course, that this lessens the Ho Yay-tastic-ness of it any less... just puts a different spin on said Ho Yay.
Fair point. I'd argue it's gone from the first to the second scenario as the series progresses.
They have what is essentially a dinner date at the end of 7x12.
What is, by all appearances, a standing dinner date, no less - it looked and played out like something they had done a thousand times before.
Many have speculated that, considering the fact that Tony's own father was completely useless, he is desperate for a "Well Done, Son" Guy father figure.
It's worth mentioning that "Team Gibbs" is often likened to a dysfunctional family unit. With Tony, Ziva, McGee and Abby all playing various sibling roles and competing for Gibbs' Approval. The fact that the former three all have glaring parental issues helps to cement this.
The writers seem to be playing up the HoYay between Tony and McGee more and more as the seasons progress. Their subplot of 7x19 is basically Tony trying to make Tim jealous by bromancing the Detective of the Week.
Also played for laughs in one episode, when Tony and McGee had to guard a dead body outdoors overnight.