Slight spoilers for Guardians of the Galaxy follow.
At the very end of Guardians of the Galaxy Nova Prime tells Peter Quill that they've discovered something about his physiology: he's only half-Terran. His mom, who we saw on her death bed at the beginning of the film, was from Earth but his dad was something non-terrestrial, and something more ancient than the Nova Corps had ever seen. This comes on the heels of the revelation that Quill had been kidnapped by the Ravagers to deliver the boy to his father, who Yondu calls a jackass. That leaves a small mystery for Guardians 2: who is Quill's dad?
This reflects the Marvel Comics character of Star-Lord, but I somehow doubt the movies will be following the same path as the books. In the comics Quill's alien dad ends up being J'Son (seriously), king of the planet Spartax. Spartax is the home of the Spartoi people, who are pretty much just humans. J'Son's not much of a character, although recent Marvel comics - in anticipation of the Guardians movie - have been giving him more panel time.
Still, it's unlikely that Guardians 2 is going to reveal that Quill's dad is J'Son. For one thing, the Spartoi aren't particularly ancient or interesting. For another, his mom tells the boy that his dad was an angel, a being of pure light. That doesn't gibe with the Spartoi being your standard space people (although I did briefly entertain the idea that she was talking about the tractor beam that we see the Ravagers use to pick up Quill later - a tractor beam that, by the way, really reminds me of the Rainbow Bridge effect from the Thor films). The reality, though, is that setting this up as a mystery when the information is available on Wikipedia doesn't make a lot of sense, especially considering how clumsily it was set up in the film.
So who is Star-Lord's dad? Talking to James Gunn at the Guardians of the Galaxy junket he told me only four people know: himself, Kevin Feige, Michael Rooker and Sean Gunn, who played Kraglin, Yondu's number two. If it was J'Son many more people would know, so I'm pretty sure we can definitively rule out Spartax as Quill's secret origin. That leaves us with some possibilities from the comics - although there's no guarantee that Gunn is going to the comics for this at all.
One possibility is that he's a cosmic being. If the Marvel Cinematic Universe is going to follow the comics, Thanos is in love with the anthropomorphic embodiment of Death, a whole new level of weird that needs to be introduced. Having Quill's dad be another one of these next-level beings would help ease the introduction. Could Eternity or Lord Order or The In-Betweener have become corporeal and sired Quill? It does seem unlikely, and it would probably make Quill way, way too weird and too close to a Jesus figure.
Or maybe his dad is an Eternal. Guardians introduces the Celestials, the giant race of ancient beings who travel the galaxy guiding (and ending) evolution on many planets. I believe that in Guardians we see the Celestial known as Arishem the Judge. In the comics the Celestials came to Earth and created the Eternals, the first race of intelligent life on Earth. In the process they also created the Deviants, a grotesque race of deformed and evil monsters. The Eternals acted as protectors of the Earth, and they eventually built a colony off world. There the scientist Kronos engaged in experiments that went wrong, turning himself into an energy being and giving his people godlike powers.
It should be noted that Kronos is actually Thanos' grandfather, so having Quill be half-Eternal is a nice way to tie him in with the larger threat facing the entire Marvel Cinematic Universe.
The Eternals also created the Inhumans, a group of secretive super-powered beings on Earth who many have speculated will be the MCU's analogue for mutants Actually the Kree created the Inhumans, but were inspired to do so after experimenting on a captured Eternal. I'm getting all my ancient astronaut stuff mixed up! Making Quill half-Eternal opens up a lot of doors for the MCU. The Eternals are ancient - most of the active Eternals are more than 3000 years old - and their direct connection to the Celestials makes them odd and intriguing. It's actually worth noting that the Celestials were introduced in The Eternals #1 in 1976.
Of the Eternals the character most likely to be Quill's dad is Eros, aka Starfox. His powers give him control over the emotions of others, and he usually uses these powers to seduce women. If this sounds like date rape, it sort of is, and he was eventually brought up on charges of sexual assault on Earth. His pelvic sorcery could certainly have been passed on to Quill. And it's worth noting: I've heard Starfox, after being on the run for his crimes, is coming back to the Marvel Comics Universe.
A geeky side-note: it would be amazing if the Eternals, a really lesser-known part of the Marvel Universe, made it to the big screen before the New Gods, DC's pantheon of cosmic beings. Jack Kirby created both, but he created the Eternals only after his Fourth World Saga at DC had been canceled. Thanos himself is more or less a knock-off of Kirby's Darkseid, and The Eternals picked up a lot of the thematic concerns Kirby had in his New Gods books. My sources tell me not to expect Darkseid in the DC movieverse until Justice League 2, so that means a Guardians 2 in 2017 would definitely have the Eternals beating the New Gods to big screens.
Could Quill's dad be Adam Warlock, a cosmic heavy-hitter whose comic book appearances almost always have him going against Thanos? Maybe, but only if Warlock is significantly changed from the comics. In the comics he is originally Him, an artificially created perfect human who ends up in control of one of the Infinity Gems (and in fact is the center of the story that revealed their existence). Adam Warlock was born out of a cocoon on Earth, and that cocoon was visible in the Collector's museum. Again, Gunn would have to be changing up Warlock in big ways to make him work as Quill's dad.
There's one other possibility when it comes to Quill's father: what if he's The Beyonder? This is really, really unlikely, but the idea of the dad being an angel and a being of pure light certainly fits in with The Beyonder's natural state. It took human male form in Secret Wars II, and was only defeated when he chose to put himself in a mortal body and was then killed. Truthfully The Beyonder is so powerful - he's god, basically - that hiring someone to pick up his son doesn't make a lot of sense... but how bizarre would that be, having The Beyonder show up in the MCU and open the door for a Secret Wars movie?