So I was thinking about why I ship Jason/Tim, and usually, I'm not very articulate to why. Well, I feel like trying (even though I'm sure my genius thoughts from the bathtub have faded, and I won't be anymore articulate than normal).
Reason 1: If any of you have ever tried to make sense of the Bat timeline (which I'm sure most of you have for fic purposes), and you look at the Robins' timeline from where Dick stops, Jason starts then dies, and when Timmy comes out of the shadows, you'll find that Tim, according to the info that he started stalking at 9, stalked both Dick and Jason for equal amounts of time (if not a bit longer for Jason considering Dick was probably more with the Teen Titans during his last few years of Robin).
With that reasoning and the fact Tim is so enamored with Dick, surely stalking Jason for about the same amount of time lead to at least some hero worship (that canon ignores now, but they didn't always: e.g. Nightwing #25, being the source I think off the top of my head and those Batman issues where Tim has hallucinations of both Robins). There was potential, which leads to my next point.
Reason 2: There was so much potential in the what ifs. You all know I love AUs, and the multiverse concept is like my favorite, so the potential of what would have happened had Jason lived? Would Tim have come out of the shadows? What if Jason had lived, but couldn't be Robin anymore? I'm sure Tim would have gone to both Dick and Jason once Batman went a little crazy (which I'm sure would still happen if Jay got seriously injured).
So many possibilities. Hell, there's even the possibilities of Tim running into Jay pre-Robin II. He was stalking Batman & Robin, and we all know that leads to Crime Alley more often than not. He could have run into that street smart kid who was jacking tires to survive. Jason wasn't always a big bundle of anger. Sure, anger is a big part of who he is, but another part of him is protecting people who can't protect themselves (and this didn't just happen because he was Robin, or he'd never have helped Batman take down Ma Gunn is first Post-Crisis storyline). And Tim was definitely a tiny little thing. Jay would have been protective because it would have been obvious Tim didn't belong in Crime Alley.
And back on the thread of what if Jay had lived, there's always the possibility that Tim could have been someone else's sidekick (e.g. Blue Beetle, Black Canary, ect.), and he and Jay would have met that way. Tim would probably still have his Robin awe, and Jason would eat that up. XD
Reason 3: Now, let's talk about how Jason came back. After the Hush and Under the Hood stuff, when he mellowed a little from Countdown, Jason does try to work with Tim. Tim, of course doesn't take the offer because of Jay's methods, but there's an effort there. A bit of a change from trying to slit his throat (and anyway, that wasn't really about Tim so much as to get to Bruce, and the fight in the Tower was more testing his replacement; it's not his fault Tim wasn't up to snuff at that point, at least against Jason's brute strength).
Ignoring Battle for the Cowl because I'm waiting for the retcon, Tim took on Jason's costume yet again. This is not the first time Tim's worn a costume of Jay's. In A Lonely Place Of Dying, Tim takes Jason's Robin costume to go help Batman and Nightwing with Two-Face. Then there's the time Tim fought in a red ski mask, which looked rather similar to the Red Hood outfit Jason where's later (which is just coincidence, but it amuses me, shhh). Now we have Tim in the Red Robin suit. Not that canon is ever gonna point out where it came from, but it was specially made for Jason by Earth-51 Bruce.
Okay, none of the reason above really connects, but shush. BUT, if you read Red Robin, you see Tim getting rather Jason like. Not to Jason's extent, but there's enough there that if they didn't have all the baggage, they'd get along at this point. More likely, if BftC and Batman & Robin issues are proven to be a Jason Todd from another Earth, and our Jason came back from wherever, I'm pretty sure Tim would begrudgingly work with him, at least to take down the fake Jason.
Miscellaneous Facts: So, Batman: the Animated Series is totally like Jason and Tim had a love child. That Tim Drake has Jay's back story, some of his anger, and the rest is some bouncy Tim with the stalkerness we all have come to love. XD
Then there's just the almost extreme opposites the boys are. Opposites attract, as corny as that sounds. Plus, Jason's the brawn while Tim's the brains. It would combined to make an interesting and effective team up.
And though I hate BtfC, some of the lines were totally Jason hitting on Tim. XD *points to her icon* Yes, that's how I'm ending this little rant. It's valid, dammit. XD And 'Join me. Be my Robin.' is totally a marriage proposal. XD Take that.