Also, the fact that L placed sixty four surveillance cameras in Light's room. And only Light's room - his other family apparently only had one. And L is seen, pretty much all the time, only watching the cameras with Light in it. This is hilariously lampshaded in the doujinshi Light Note, where it explains that the reason why L kept stalking and watching Light obsessively (and rather unreasonably) was not because he inexplicably suspected him to be a serial killer but because he had a big crush on him.
On Light's part, upon discovering L's cameras he resolves the situation by... buying porn?
There is one interesting scene in the manga after Light is "proved innocent" (Volume 7, chapter 55, pages 60-61). L decides that Light can stay investigating the Kira case if he wants to, but Misa should leave. Light then asks L if he is allowed to see her outside the headquarters, with a very surprised L asking him why he suddenly wants to be with her. Light tells him he may have fallen in love with her and... well, we know these two are always getting suspicious about everything the other does, L especially. But the way the whole scene is drawn it's suspicious to say the least, especially with those close ups of Light's repenting face when he is about to confess his feelings for Misa, and L's blank face at the end. And then L starts thinking about Higuchi, so it's not like he started tying loose ends with the information he just received.
In the manga when Light is getting his memories back (and is about to close the loop and spring the trap that will lead to L's death) he shows a moment of hesitation where he's wishing he had more time with L you know, just to get closer, to win his trust...
Of course, the entire scene isn't helped by how the anime made it seem like L had a foot fetish. Both Light and L are soaking wet, drying themselves off, and their dialogue and actions go something like this:
(L kneels down in front of Light and takes his foot in his hands)
Light: What are you doing, Ryuuzaki?! L: At least allow me to atone for this. I'm not all that bad at it, you know. Light:(looking away) Do as you please. (L presses Light's foot, and Light cries out) L: Oi, you'll get used to it quickly. Light: You're still wet. (wipes L's soaked bangs with a towel)
Oh and Light looks very annoyed when L stops... massaging his foot.
Episode 26. ( A depressed Light keeps seeing L's ghost. At one point the L ghost / hallucination silently mouths something that looks suspiciously like "I love you." In the scene immediately following Light very unenthusiastically asks Misa to move in with him.)
Also, Light continues to obsess about L years after L is dead. "The real L would / would never X..." Not to mention that his last thoughts are of L...
It's a few days after L's funeral that Light's moping around the HQ desolate that "there's no challenge with L gone". Remember how heavily he's motivated by boredom; by second arc, he remembers L almost fondly!
Then there is Light's initial reaction when Rem finally kills L. He looks very shocked. There's even a hint of tears. Of course it's gone in an instant replaced by the world's most disturbing Slasher Smile as L dies in his arms and he rejoices in Kira's victory. Light is a very good actor but at that moment there was no one to act to.
In the manga when L breaks out the handcuffs and states "I'm not doing this because I want to..." it comes off as rather sarcastic considering he's saying it with * SEXY POSE* and a wicked grin on his face.
Every room at Taskfroce HQ is monitored... EXCEPT for L and Light's bedroom...
When he goes to face Near and thinks that he's defeated Near's final maneuver, he remarks that Near is "far below L." This indicates that he does respect L on some level.
Then there's that fight Light and L had while handcuffed together which involved pulling each other's shirts up and having L's pants fall down so you can see the waistline of his boxers...
Apparently L gave Light his personal cell phone number...
When phoning up Matsuda, L calls himself "Asahi", Light (and Mr. Yagami's) alias and L is apparently cool with letting Light use his name as well...
In one of the Omake, Light is arguing with Ryuk on how strawberries are definitely more of a turn on than apples... (Remember who has that as a Trademark Favorite Food... "I'll give you this strawberry if you keep it a secret, okay?")
"Let's all be friends together!" when Misa forces Light and L into a Circle of Friendship—Light and L chose to hold hands, are facing each other, and Light looks very... happy in that scene... 
As Lampshaded by Misa the fifty day confinement is a bit... suggestive of something, (though it is Light that L is primarily interested in) especially how Light is tied up and pleading to be let out-looks like Light forgot the Safe Word.
Then there is the the instance when Light manipulates Rem, persuading her that for Misa to be happy L has to die. At first Rem gives no response and Light says sarcastically "oh, that's too bad..." he was acting like he didn't expect it to work, like if L catches Misa now it's not on his hands but then to Light's surprise Rem AGREES to it, perhaps reacting when Light ends his Circling Monologue and takes his hand off Misa's shoulder as if to say 'I won't love her unless L is dead'. Light gets a very stricken look on his face and thinks " L will dieTHIS EASILY?!" Rem is ready to kill L right then and there but Light immediately backtracks and gives a Hurricane of Excuses why it would be bad to kill L right away.
L succeeds in getting under Light's skin when he tells him "I feel as if you're the first friend I've ever had." Light continues to obsess about L as he walks home up until he's glomped by Misa, sounding very much like a Tsundere all the way as he curses L's name (or rather his alias). Ryuk mocks this development in a very suggestive tone:
Light: That DAMN Ryuuzaki!
Ryuk:Friend. *snicker* He's your friend. But that's a good thing, isn't it, Light?
Yeah, that DAMN Ryuuzaki, saying he's my friend. It's not like I like you or anything!
Also during the Yotsuba arc when Light has lost his Kira memories and the knowledge that L is his enemy, you'd still think he'd be a bit upset with L for confining him for 50 days and making his father carry out a mock execution, yet when L ends their confinementLight seems not to hold any grudge against L for locking him up and indeed seems quite thrilled about the idea of being with L 24/7.
When L meets Light at the campus for the last time before his confinement and Misa appears, L starts giggling and says something to Light that has different fansub translations. It can be either "Light-kun, I envy you" or "Light-kun, I'm jealous". He makes it clear after saying that that he was being jealous-envy of Light's "girlfriend", being a fan of her, but in the moment he says it, it's not clear if he's saying he is jealous of Light or Misa... It doesn't help that, in the manga version only, Ryuk is shown to have the biggest WTF-did-he-just-say-what-I-think-he-said face ever, suggesting that he captured the ambiguity of the statement as well.
During L's death scene even though it was probably an act how bout when Light catches and holds L in his arms following him falling over once his heart gives out? Also upon realizing that L is dead-he SCREAMS. Makes you wonder if it'sallan act...
There are hints that Light grieves the loss of L. In the days following L's death there's an interesting scene where Light and Ryuk are up on the roof of Taskforce headquarters overlooking the city.
Ryuk: So you've finally settled the score with L, huh?
This trooper was distracted and read "So you've finally score with L, huh?"
Light's voice in that scene is not elated with victory but instead sounds kind of sad, disappointed, empty... in that same scene he looks very depressed as he grasps for a chain that is no longer there (both literally and figuratively) and then quite visibly SNAPS and throws himself into his "work" like never before...
There is another deleted scene from the OVA's where L is talking to the children from Wammy through the monitor and they ask him if he is afraid of anything. L tells them that he is afraid of many things, but the thing that hates the most is being lied to. Now, go watch the scene under the rain form episode 25 and tell me, after knowing this and shipping Light/L if the scene is not even more of a Tear Jerker now.
Which is kind of hypocritical, considering what a shameless liar L is himself.
In the Alternate Continuity of L: change the WorLd Light isn't even alive in this universe, and there is still plenty of fodder for shippers, starting with the way L wears Light's watch in "rememberance," strengthened by the quote "Light, it hurts... My heart-", and ending with his offering at Light's altar.
In the manga (Volume 2 chapter 16 pg 185) there is an ambiguously flirty exchange between Light and Yamamoto (a male classmate of Light's / an extremely minor character who gets about as much pagetime as Matt) during New Year's, where Light points out Yamamoto hasn't sent him a card, and is told "Sorry Light, I only give cards to girls."
There's lots of Les Yay between Misa and her Shinigami Rem, mostly from Rem's side though, who not only loves her but is willing to die for her.
Let's take a look at Relight, shall we?. When the camera shows Ryuuk notebook at the end we get to see that it seems to be tattered and unused for a looong time. What's wrong, Ryuuk? Your old owner's death have leave you depressed?
Ryuk's character design in the anime constantly features a full-heart drop earring, but in the Relight special, after Light's death, the earring becomes a broken heart. This is hard to catch the first time through, but it is there.
Sayu occasionally shows some interesting tendencies, like grabbing at Light's tabloids to look for dirty pictures or commenting that she can see Misa's underwear shortly after meeting her or saying that Misa is just her type.
How did we get this far without commenting on Mello and Near's odd concern about each other? There is a whole Foe Yay aspect to it, but Mello is so overly concerned with everything Near does it comes across as stalkerish. When he talks about Mello, Near is likewise very complimenting and admiring, and toward the end says he and Mello should have been partners, and that it would've led to great things.
Near is the only person with a picture of Mello. Just something to chew on...
There's also Matsuda and almost every other male character. In regards to Light and L he really looked up to them, to the point of obsession in some cases.
"Your reasoning is not actually reasoning but...desire. Your desire. Light was Kira, but you liked Light, didn't you, Matsuda?" And what does Matsuda say in return? "Desire...it may be so."
The subtext of that scene is written directly as text in some of the manga's Spanish translations. Ide's question is translated as "Te gustaba Light, ¿verdad?". The verb "gustar" used towards another person, at least in some Spanish speaking places, has the meaning of being sexually attracted to somebody. To like somebody as a friend or as a person would require another verb, like "agradar" or "simpatizar".
And in chapter 107 as Light begs for his life Matsuda appears to feel sorry for him.
There are strong hints that Matsuda is bisexual, if not just outright gay - though he does seem attracted to Sayu in the second half of the series. He is known to be quite "fond" of Light, following him in a manner that could easily be indicative of a crush. He shows no jealously whatsoever when seeing Light with women, but this may just be him accepting that Light is straight and would of course have no interest in him. His actions near the end as he shoots Light and screams at him almost look like the reaction of a lover learning the truth about his significant other. And then there's his throwing an arm around a blushing male coworker...
Okay, what about MIKAMI people!? The guy is was COMPLETELY obsessed with Kira/Light. So much so that (in the anime only) he commits suicide via PEN and in the manga kills himself in jail when he realizes Kira has lost and it was all his fault.
If you ship L x Light (and are still watching by the second season) it makes sense to ship Mikami as Light's Replacement Love Interest especially considering that Light's selection process basically consisted of him scanning the crowd of Kira supporters and choosing the first tall, wild haired, Eerie Pale-Skinned Brunette his eye happened to land on...
Mikami's adoration for his God is totally canon: 
Light and Mikami get REALLY excited when talking to each other on the phone (complete with some very EXTREME facial expressions.)
The movieverse gives us F x L L writes his own name in the Death Note after learning that F is dead. Also from the movies L and Hideaki Suruga have a "mommy and daddy" vibe when taking care of the orphans.
In the first episode a surprising number of men seem to be checking out Light. At each crossing he stops at, someone is giving him a sideways glance.
Also in the first episode Light's English teacher seems way too interested...