1. Jack Harkness' Future
This is the biggie. The one you've been hoping for every time you click next. Well here it is. One throwaway line that changed the perceptions of a character forever. Clearly Jack wasn't originally intended to be the Face of Boe and I suspect it wasn't even a fully formed idea when the Face died. But come the end of Series 3 he revealed his old nickname was the same as the big head in a jar, setting the internet alight with speculation. Jacks appeared a couple of times since on the main show and this wasn't mentioned at all, suggested Davies had little interest in confirming or denying the rumour. It is admittedly more fun to keep it open, but there's nothing quite like closure. Its believable that the immortal Jack would eventually change in appearance (and reproductive system) to the extent where he was alien to what he originally was, but given the variable rules of Who it cant be taken as gospel until theres some proof. John Barrowman has been consistently rumoured to be to the series, but given no one from the Davies' era (Tennat excluded) has been in Moffats Who thisll be something thats never going to be explained beyond the hint we got.
Potential Solution: Just say it's true. It's a lot more awesome that way.
So there you have it. All those lost plots, all that potential. Are there any of these you were particularly sad to see dropped? And are there any more I've missed? Head down to the comments below and have your say.