Supernatural Season 2-3 Timeline
Season 2 | Season 3

I've done my best to parse out the when of the Season 2 and Season 3 timeline. We've gotten very few concrete dates, and the one episode that does give a specific date is 2x16: Road Kill (February 22, 2007), which... really doesn't make much sense in the bigger scheme of things, unless Dean rebuilt the Impala in under two days and gave it the ability to teleport instantly back and forth across the country.

Lum came up with the ever-so-spiffy idea of time-shifting it earlier in the season to avoid a complete timeline snafu, and since there are no references in that episode to any other eps, I thought that was a fantastic idea. Drive times are not included in the number of days spanned by a given episode.

Events in italics are my best guess.
Year Date/Timeframe Episode Locations Notes
2006 Oct. 31-Nov. 2 (1.22 Devil's Trap) Salvation, Iowa
Lincoln, Nebraska
Jefferson City, Missouri
Unknown rural locations in South Dakota & Missouri
November 2 (Pilot) 23rd anniversary of Mary Winchester's death
1st anniversary of Jessica Moore's death
November 3-4 2.01 In My Time Of Dying South Dakota spans 3 days
November 4 or 5 South Dakota burning of John's body (ELaC)
November 5-13 South Dakota "Over a week" spent at Bobby's (ELaC)
November 13-16 2.02 Everybody Loves a Clown South Dakota
Nebraska
Medford, Wisconsin		 spans 4 days
South Dakota approximately 4 weeks to repair the Impala
December 5 anniversary of Mary Winchester's birthday
Mid December 2.03 Bloodlust Red Lodge, Montana spans 2 days
Mid December 2.04 Children Shouldn't Play with Dead Things unknown, possibly Montana spans 4 days
Mid December (2.10 Hunted) Lafayette, Indiana Gordon kills Scott Carey. Scott says he started hearing from the demon "a little over a year ago." In "Hunted," Gordon says he killed Scott "about a month ago."
Late December 2.05 Simon Said Nebraska
Guthrie, Oklahoma		 spans 2 days. I'd say after Christmas, since there are no decorations. And boy, it's warm in Guthrie this winter...
Nebraska a day or two at most - Sam and Dean are still at the Roadhouse
2007 Early January 2.06 No Exit Nebraska
Philadelphia, Pennsylvania		 spans 4-5 days
Early January 2.07 The Usual Suspects Baltimore, Maryland spans 4 days. Ballard says that it's been "about a year" since Jess died, and that Sam is still 23, so it's before May.
At the beginning of Crossroad Blues, Sam is reading about Dean in the Federal Database. Likely, only a few days have passed.
Mid January 2.08 Crossroad Blues Greenwood, Mississippi spans 2 days
Unclear how much time has passed.
Mid January 2.09 Croatoan River Grove, Oregon spans 2-3 days
contiguous with next episode
Mid January 2.10 Hunted River Grove, Oregon
Lafayette, Indiana
Peoria, Illinois		 spans 4-5 days
January 24 Dean's 28th birthday
anniversary of Jess's birthday
Peoria, Illinois 1 month spent hunting for Ava (dialogue from "Playthings")
Mid February 2.11 Playthings Peoria, Illinois
Cornwall, Connecticut		 spans 4-5 days. Sam gets his cast off after this episode.
February 22 2.16 Roadkill Highway 41, Nevada Stated by Molly, which, yeah, totally fucks up the timeline. *g* Which is why I'm putting it here. Spans one night. (thank you to Luminosity and harrigan for the collective brainstorm.)
Late February 2.12 Nightshifter Milwaukee, Wisconsin spans 3-4 days
Perhaps less than a week, almost certainly less than two, passes between these episodes, since Sam still has Dean on "lockdown."
Early March 2.13 Houses of the Holy Providence, Rhode Island spans 3 days
West Texas Some time seems to pass here. They go on another job in West Texas, then Sam is missing for over a week before demon!Sam calls Dean.
Mid March 2.14 Born Under a Bad Sign Duluth, Minnesota
South Dakota		 spans 2 days
Mid March 2.15 Tall Tales Springfield, Ohio spans a week
March 31-April 6 2.17 Heart San Francisco, California spans 6 days. The full moon is on Monday, April 2. Thanks, harriet_spy!
Late April
(Early April)*		 2.18 Hollywood Babylon Los Angeles, California spans 4 days. L.A. had a cold front and rain on April 20. Positively Canadian!
Last week of April
(Mid April)		 2.19 Folsom Prison Blues Green River County, Arkansas spans 4 nights and 3 days
Early May
(Late April)		 2.20 What Is and What Should Never Be Joliet, Illinois
(Lawrence, Kansas)		 possibly spans 2 nights and 2 days, but unclear
May 2 Sam's 24th birthday
End of June
(Late April/Early May)		 2.21 All Hell Breaks Loose, Part 1 Cold Oak, South Dakota
Nebraska

spans 2 nights and 1 day. Sam tells Ava she disappeared "five months ago."

Sam also says that all the psy-kids are 23 years old, which throws things off by as much as two months if true. It's a toss-up: either Ava disappeared three months ago, not five, or Sam is generalizing about the collective age of the psy-kids for the simplicity of explaining why they're all in Cold Oak. The second explanation makes more sense to me than the first, but YMMV. If you choose to go the other way, the alternate date possibilities are in blue to the left.

NOTE: The concrete date shown on the motel receipt in 3.15, "Time Is On My Side," gives support for the June date. The concrete date given in "Ghostfacers" is February 29th, which contradicts the receipt date and supports the April/May 2 date. At this point I'd say it's impossible to completely reconcile the timeline of S2-S3, so follow your bliss.
End of June
(Early May)		 2.22 All Hell Breaks Loose, Part 2 South Dakota,
southern Wyoming		 spans 2 nights and 1 day. Contiguous with previous episode.
  Five days pass between the end of Season 2 and the beginning of Season 3, as stated by Dean in "The Magnificent Seven."
Early July
(Early May)		 3.01 The Magnificent Seven Oak Park, Illinois
Lincoln, Nebraska		 spans 2 nights and 1 day
Indefinite time passes, possibly about two and a half to three weeks .
Mid July
(Late May)		 3.02 The Kids Are Alright Cicero, Indiana spans 2 days and 1 night
Kubrick states that Sam was last seen in Nebraska "three weeks back."

This could be referring to AHBL, but I'd say it's more likely that he got this information through Tamara. The opening scene of 3.03 seems to indicate Sam's encounter with Ruby is recent, as though not much time passes between 3.02 and 3.03. It's possible, however, that some or all of the missing three weeks occur here, and Sam delayed telling Dean about Ruby.
3rd week of July
(Early June)		 3.03 Bad Day at Black Rock (state prison, Indiana)
Black Rock, New York
Connecticut
Queens, New York		 appears to span 4 days and 4 nights. Appears to follow shortly after previous episode, perhaps no more than a day.
Late August
(Late June)		 3.04 Sin City South Dakota
Elizabethville, Ohio		 appears to span 4 days and 3 nights. Sam states that it's been two months since the opening of the Devil's Gate.
Two months pass between these episodes. Or, if you're following the timeline in blue, four months.
Late October (October 23-26) 3.05 Bedtime Stories Maple Springs, New York appears to span 4 nights and 3 days, assuming Sam and Dean read about the "psychotic killer" the day after the attack on the guys at the construction site. Dean states it's close to Halloween. Sam says, "The moon's full this Friday," which would be Friday, October 26, so the episode takes place earlier that week. Sam goes to the crossroads under a full moon, so that makes it October 26, 2007.

This is the first semi-concrete date we've gotten in quite a while. Either it's been four months or six months since Dean made his deal, depending on how you interpret Sam's dialogue in "All Hell Breaks Loose."
Late October/
Early November		 3.06 Red Sky at Morning Eastern seaboard (possibly near Hilton Head; more likely Newport, Rhode Island)

ETA: And possibly, my earlier guess of Cape Cod was right, since Gordon mentions Mass. in 3.07.		 appears to span 5 nights and 4 days. Unclear how much time has passed since the previous episode, but probably not more than a few days, since it seems unlikely Dean kept quiet about the missing bullet for longer than that. Um... we'll ignore the fact that the moon is full again, shall we?

The only references made to location are "the bay," and the "Sea Pines Maritime Museum." Sea Pines is a resort on Hilton Head, SC. However, the name "Sea Pines" could indicate any number of coastal areas, and mumbles11 spotted Rhode Island plates on one of the cars.
November 2 (Pilot) 24th anniversary of Mary Winchester's death
2nd anniversary of Jessica Moore's death
November 4 ("In My Time of Dying") 1st anniversary of John Winchester's death
Early November 3.07 Fresh Blood Unknown large city, probably New York. All the cars in the ep had New York plates. spans 3 nights and 3 days. Not much time has passed since the previous episode -- maybe a couple of days. Gordon says to Bela, "I know you were just in Massachusetts, and I know you were with the Winchester boys."
December 5 anniversary of Mary Winchester's birthday
Late December 3.08 A Very Supernatural Christmas Ypsilanti, Michigan appears to span 3 nights and 2 days. Presumably, the last scene takes place on Christmas.
2008 January 24 Dean's 29th birthday
anniversary of Jess's birthday
Late January 3.09 Malleus Maleficarum The town is called Sherwood, but no indication of region or state is given. appears to span 3 nights and 2 days.
Late January-Early February 3.10 Dream a Little Dream Pittsburg, Pennsylvania appears to span 6 days and 5 nights.
February 5-6 3.11 Mystery Spot Broward County, Florida Heh. Appears to span one day... a lot. I'm going to call this February 5-6 because you can see on the clock radio that the date on Tuesday is a 5, and February 5th falls on a Tuesday. Hey, a concrete date!
Mid February 3.12 Jus In Bello Monument, Colorado Spans one night and one day. Gotta completely ignore the date on the photo shown from "Night Shifter," because it reads 09/10/06, and that would place it two months before John's death. (Note: an official canonical spelling of Henriksen's name!)
February 29 3.13 Ghostfacers Unknown, not Texas Spans one night. This episode is definitively placed on February 29th, 2008, and Sam states that Dean has two months left to live. Contradicts the date on their motel receipt from "Time Is On My Side," which is mid-June. Sam, seriously, does he have two months or four months left? Poor boy is so distraught he can't keep it straight.
March 3.14 Long Distance Call Milan, Ohio appears to span 3 days and 3 nights.
May 2 Sam's 25th birthday
Mid June
(Mid April)		 3.15 Time Is On My Side

Erie, Pennsylvania
Canaan, Vermont

 appears to span 4 nights and 3 days. The receipt that Bela steals from Dean shows them checking into the Erie motel on June 11, 2008. See note.
End of June
(Early May)		 3.16 No Rest for the Wicked South Dakota
New Harmony, Indiana		 In 3.15, Dean says they're three weeks out from his due date.