In order to really determine the timeline we first need to figure out exactly how old Amy is and when she was born.
We know that the cracks in the universe from season 5 revolve around a specific date: June 26th, 2010. This was in fact Amy's wedding day. We also know that the Doctor picked up Amy on the eve of her wedding. So therefore June 25th, 2010 is when Amy began traveling with the Doctor. When the Doctor showed up that night, she stated he was 2 years late after the events of The Eleventh Hour, so that episode primarily took place in 2008. When the Doctor showed up in 2008, Amy mentioned that he promised he would return after 5 minutes, but instead took him 12 years. So 1996 is when the young Amelia Pond first met the Doctor (She mentioned she was 7) meaning she was born in 1989. With all of that out of the way, this is what I believe the timeline is: (a) denotes alternate timeline
1989 - Amelia Pond is born
1996 - Seven year old Amelia Pond is praying to Santa asking for help with the crack in her wall. The Doctor crash lands in her back yard and after investigating the crack in her wall, promises to return in 5 minutes. Amelia runs to get her suitcase so she can travel with the Doctor and patiently waits outside*(The Eleventh Hour)
1996(a) - Young Amelia goes to the museum to see the Pandorica and rescue her future self (The Pandorica opens)
2008 - The Doctor returns and find Amelia (now going by the name Amy) has grown up and that his 5 minutes turned into 12 years. They deal with Prisoner Zero and the Doctor leaves promising to return (The Eleventh Hour)
June 25th, 2010 - The Doctor returns again to pick Amy up but realizes he is late again. They take off in the Tardis for their adventures (The Eleventh Hour)
The Doctor and Amy travel together
- The Beast Below
- The Victory of the Daleks
- The Time of Angels
- Flesh and Stone
June 25th, 2010 - Amy asks the Doctor to return her back to this date and shows him her wedding dress and that she is to marry Rory the next day. (Flesh and Stone)
June 25th, 2010 - That same night, the Doctor crashes Rory's Stag party and takes them to Venice for a romantic trip. (The Vampires of Venice)
The Doctor, Amy, and Rory travel together
- Amy's Choice
- The Hungry Earth
- Cold Blood
The Doctor and Amy travel together
- Vincent and the Doctor
- The Lodger **
- The Pandorica Opens
- The Big Bang (a)
June 26th, 2010 - Amy and Rory's Wedding. The Doctor is remembered back into existance
The Doctor, Amy, and Rory Travel together
- A Christmas Carol
- Off screen adventures between April 2010 and February 2011??
February 2011 - The Doctor drops the Ponds off. It is referenced in "The Impossible Astronaut" that they haven't seen the Doctor for 2 months
April 2011 - The Ponds get an invitation to meet in America with coordinates. (The Impossible Astronaut)
April 19th, 2011 - Amy and Rory go shopping at a department store possibly in preparation for America. The Doctor spots them from the distance as a girl asks for Amy's autograph since she is now a model for a prefume line Petrichor which means the smell of dust and rain (Closing Time) ***
April 22nd, 2011 - Amy, Rory, and River watch as the Doctor is Shot by an astronaut in a spacesuit (The Impossible Astronaut)
April 22nd, 2011(a) - Alternate timeline where River does NOT kill the Doctor at Lake Silenceo (The Wedding of River Song)
The Doctor, Rory, and Amy's travels
- Day of the Moon
- The Curse of the Black Spot
- The Doctors Wife
- The Rebel Flesh
- The Almost People
- A good Man Goes to War (River takes the Ponds home)
September 2011 Amy and Rory reaches out to the Doctor by creating a large sign with his name in a corn field. When he arrives, Amy asks if he had found Melody since he's had all summer so I am guessing it's roughly September at this point (Let's Kill Hitler)
The Doctor, Rory, and Amy's travels
- Night Terrors
- The Girl who waited
- The God Complex
September 2011??? - The Doctor drops Amy and Rory off after the God Complex and also gives Rory a new car and the Ponds a new flat and takes off. They don't hear from him for a while and they presume he's still dead after all that they did.
December 2013 - The Doctor visits Amy and Rory around Christmas and Amy scolds him for not visiting sooner since it had been 2 years that he was "dead" (The Doctor, the Widow, and the Wardrobe)
April 2016 - Pond Life 1
May 2016 - Pond Life 2 (From the Doctor's POV Dinosaurs on a Spaceship happened recently)
June 2016 - Pond Life 3
July 2016 - Pond Life 4
August 2016 - Pond Life 5
August 2016 - Asylum of the Daleks (Rory gives Amy divorce papers)
June 2017 - Amy, Rory, and Brian get picked up by the Doctor and taken to a spaceship for an adventure. Amy mentions it has been 10 months since they last saw the Doctor. (Dinosaurs on a Spaceship)
July 2017 - The invasion of the Cubes begin (The Power of Three)****
October 2017 - Amy becomes a brides maid for her friend (The Power of Three)
June 26th, 2018 - Rory and Amy's wedding anniversary. They throw a party which the Doctor secretly crashes and takes them for an adventure (The Power of Three)
The Doctor, Amy, and Rory travel together
- Savoy Hotel
- Henry VII
- "A Town Called Mercy"
June 26th, 2018 - Back at the dinner party but they've been gone for 7 weeks. (The Power of Three)
September 18th, 2018 -
The Angels take Manhattan Not aired at the time of writing however, set reports show Amy Reading a newspaper with this particular date.
* This one is a bit of a spoiler/speculation
Moffat has said that in "The Angels take Manhattan" there is a tie in to "The Eleventh Hour". There is a scene at the end where it is morning after young Amelia has been waiting for the Doctor all night outside sitting on her suitcase. We hear the Tardis engines as she looks up and smiles, and then the scene fades to older Amy on her wedding night hearing the same sounds. There is speculation that there will be a post credit scene after episode 5 where the Doctor goes back to visit young Amelia
** In the Lodger on Craig's fridge, there is a advertisement to see a Vincent van Gogh exibit March 17th - August 20th
*** In the episode "Closing Time", Craigs newspaper reads April 19th, 2011. Most people believe that since Petrichor was the psychic password in "The Doctor's Wife" which happens later on, it was thought that chronologically for the Ponds, "Closing Time" came after "The Doctor's Wife" in terms of what the Ponds experienced. However, I believe that the psychic password was chosen by the Tardis due to knowing Amy's perfume line, and not the other way around (The perfume line coming from the Tardis Psychic password)
**** In "The Power of Three", Amy mentions in the begining that it has been 10 years since the Doctor was in their lives. In 2008 they dealt with the Atraxi so 10 years would mean 2018. However, I think she rounded up from 9 years because she was either just rounding for the heck of it, or she was counting the amount of time she spent with the Doctor traveling + the 9 years. At any rate, it couldn't be 2018 at the start of the episode because it takes place over an entire year, and "The Angels Take Manhattan" takes place in 2018 (Amy reads a newspaper while they have a picnic).
With all of these time gaps, it's easy to see the theme with the Doctor and the Ponds. He doesn't seem to be able to show up at the right time which leads to the whole "The Girl who Waited" thing that Amy has doing for her.
Anyways, this is the best I could come up with, if you see any errors please let me know