Hikaru and Kaoru seem to flirt when they aren't serving customers as well. They can be seen holding hands or resting against each other countless times, they share a bed, and apparently used to enjoy scorning the girls that fancied their opposite.
Kaoru gives up Haruhi for his brother's happiness.
Doesn't help that he gives her up by saying (more or less) "I love you, but Hikaru is more important to me". The next chapter then opens up with Kaoru kissing Hikaru's cheek (same thing he did with Haruhi) "in conmemoration of [his] unrequited love"
Oh, and back on the subject of them sharing a bed. When they do Kaoru wears minimal clothing while Hikaru doesn't wear anything.
Mori and Honey have their moments in the absense of clients as well- See the episode where Honey has a toothache and Mori tackles Honey to a sofa and gets on top of him when looking for the cavity causing the fangirls to Squee loudly. And Mori's panic when Honey gets lost in Kyouya's family's park.
This is also what the girls think they're seeing when Kasanoda, who joined the club as a customer, picks Haruhi to be his favorite.
Speaking of Kasanoda, there's definitely something between him and his servant Tetsuya, at least on Tetsuya's side.
Haruhi herself has more than enough Les Yay with the Lobelia girls. They immediately can tell that she's a girl, despite her wearing the male school uniform, because they saw she had beautiful "maiden eyes". They also tend to be way too touch-feely with her, caress her skin and saying that it is so soft and beautiful, and the leader, Benio, acts gentlemanly towards her, kisses her hand, disregards her personal space, and tries to take her First Kiss. When it's revealed that she already had her First Kiss (albeit accidentally) with a girl, Benio tries to take Haruhi's second kiss. It's all enough to make Tamaki jealous and actually yell "Don't be touching my Haruhi without my permission!"
Plus at the academy Benio goes to she has hordes of female admirers who have made clubs dedicated to her, follow her around devotedly, and Squee loudly when she flirts with them.
There's also some slashy overtones between the leader of the Host Club Tamaki and his best friend and second-in-command Kyoya. Tamaki likes to refer to himself as the "daddy" of the club, and Kyoya as "mommy". And there was a scene in the manga where one of them was giving the other a backrub.
Then there's the flashback episode where they first meet and Kyoya is going crazy over dealing with Tamaki while trying to act normal. His sister notes that she has never seen Kyoya getting so worked up over someone before. Then at the end when he starts acting normal, it reads like a coming out story.
In between flashbacks of his relationship with Tamaki, Kyouya is shown painting a flower. The flower becomes a rainbow as he comes to care for Tamaki.
Not to mention the pains Kyouya goes to in order to appease "Daddys" every whim.
Tamaki's big decision in the finale of the anime was due to Kyouya's reprimanding him for his frivolty.
Even the actors see it — on the DVD, there's a scene in the outtakes where Kyoya says "What is it... Daddy?" in an almost seductive manner, and his voice actor breaks out of character seconds after saying the line perfectly to splutter and protest ("Really?!").
In the January 2011 special, I don't really remember the details, a girl asks Tamaki and Kyouya "Aren't you guys close? Are you homos?".. Kyouya didn't like that.
There is also Kaoru and Kyoya. When the two had to spend more time together investigating certain things involving certain people's mother, Kaoru once comments something along the lines of being surprised of how cute Kyoya can be, to the other's anger. (sorry, can't find the exact chapter).
I think it's Chapter 47
Kyoya: As long the people we care about understand us, the other stuff doesn't matter. Don't you agree?
Kyoya:Why are you making that face?
Kaoru: Um, yeah...I agree...I just realised for the first time that you are really cute.
And then in chapter 73 of the manga, there's a whole slew of it including Kyoya waking up to find Kaoru in his bed (fully dressed, on top of the covers, reading a book), Kaoru blushing as Kyoya changes clothes and Hunny asking if Hikaru is mad because "Kyo-chan stole your Kao-chan."
In Operation: Hikaru and Haruhi's First Date the two share a scene apart from the group that almost seems as though they're parents watching their children. Does the Host Club have a new mommy?
Renge unintentionally has this towards Haruhi, but to be fair she doesn't know Haruhi's The Not Secret.