UPDATED, 10:00pm
So where are we at the end of a long day of reports--ours and others'-- flying across the World Wide Web about the Lee/Halladay stunner? Not quite there, it appears, but headed in the direction of a huge trade.
A baseball source told the Inquirer tonight that a deal was not totally done. There were several other indications that it was close.  With a contract extension to be worked out, medical records to be reviewed, and three teams needing to make final decisions, it is no surpise that this is taking time. The names batted around as future Blue Jays in various reports were pitchers Kyle Drabek, outfielders Michael Taylor or Domonic Brown. CSNphilly.com had the first report of Drabek being included, which was later followed up on by the Toronto Sun. 
Ruben Amaro did not respond to phone calls seeking comment today, and team president David Montgomery said he "could not comment." It is the Phillies' policy never to publicly address trade talks. 
Keep this in mind: Even if the Phils lose Drabek in this deal, they would be surrendering less than the package requested in July of Drabek, Brown, J.A. Happ and Anthony Gose for Halladay.
Baseball America considers Drabek a potential no. 2 or 3 starter, and wouldn’t you give that up to get Halladay? We also know that both teams place a higher value on Brown than on Taylor—so if Taylor is a part of this deal instead of Brown, that is considered a discount from the July offer.
The AP reported today that Happ, Brown and Joe Blanton took physicals in Philly today, but there were no other indications that those players were involved.
This information is all tentative and speculative because a deal has not yet been finalized. There are indications that an official announcement could come within the next day or two. Until that time, anything can happen.
Toronto Blue Jays pitcher Roy Halladay and his agent have checked into a Philadelphia-area hotel, according to two Inquirer sources.
It is not known if a trade sending Halladay to the Phillies is imminent, but if Halladay and the Phils are negotiating--as is indicated by the pitcher's presence in Philadelphia--that would suggest that the Phils and Blue Jays are far enough along in talks for Halladay to discuss a potential contract extension with the Phils. Halladay has one year remaining on his contract before becoming a free agent.
The Phils have long been linked to Halladay, and were actively involved in trade talks last July, before the team acquired lefthander Cliff Lee from Cleveland.

UPDATE, 3:04--  The plot thickens: Foxsports.com has added that the Phils are in talks regading a potential three-team deal that would send lefthander Cliff Lee to an unnamed club.  This makes sense for a number of reasons:

--Lee is owed $9 million next year, and the Phils need to clear payroll to sign Halladay.

--Lee will be a free agent after this season, and if he tests the open market the Phils would find it difficult to re-sign him, given their already robust payroll.

--Acquiring Lee may net the Phils some of the prospects requried to complete a deal, without having to give up players like pitcher J.A. Happ and Kyle Drabek, outfielders Domonic Brown, Michael Taylor and Anthony Gose.

UPDATE, 5:03pm

Cliff Lee's agent, Darek Brauneker, says he has not heard anything from the Phillies, Blue Jays, Mariners or anyone else today.

Multiple reports--SI.com, I believe, was the first to confirm it--have Halladay and Lee involved in a three-way that would send Lee to Seattle. A bunch of other names are surfaced, but reports are conflicting--some have Domonic Brown going to Toronto, while others have it as Michael Taylor.  Pitcher Phillippe Aumont would reportedly be going to Toronto from Seattle.  It should be noted that none of this is confirmed.  We know that both the Jays and Phils liked Brown more than Taylor in July.

Brauneker has spoken with Lee today.  "He is obviously aware of the situation,' Braunker said.  "There must be something to it."

Brauneker, understandably, treaded carefully when asked if Lee was disappointed.  "He certainly enjoys being in Philadelphia.  There was not much for him not to enjoy."

The Phils and Lee engaged in preliminary talks about a contract extension last week.   "We had a positive dialogue," the agent said.  "All of the dialogue has been very positive on both sides."