In a year that had everything, the biggest shock was that Thomas was the only coaching casualty while Carlton's Denis Pagan and Geelong's Mark Thompson lived to fight another day despite appearing set to join the AFL's "sacked coaches club".
The Blues picked up their third wooden spoon in five years, amid continuing off-field problems, and Geelong plunged from premiership favourites to also-rans in the space of two months yet Pagan and Thompson remain in charge while Thomas was sacked, despite steering the Saints into their third successive finals series in 2006.
Thomas, the second-longest serving coach in St Kilda history having been at the helm since the shock departure of Malcolm Blight in mid 2001, paid the price for the Saints' loss to Melbourne in the first week of the finals.
While the Saints said that Thomas left the club by "mutual consent", Thomas made it clear that he never expected to be dumped when he attended a board meeting just days after the loss to the Demons.
"I had a fair inkling that I would be coach, but things change … we have to move on pretty quickly," he said.
"The board firmly believes the club is heading in a different direction and I will have to live with it. I still think I am the right bloke for the club but the club has made the decision to head in another direction."
Thomas' effort in getting the Saints to the finals in 2006 was even more creditable considering the club suffered injuries to key players, including a season-ending knee injury to star midfielder Lenny Hayes in round nine, a fractured skull to Justin Koschitzke in round six, continued knee problems for rugged forward Aaron Hamill while defender Matt Maguire broke his leg.
But just as surprising as Thomas' departure was the man named as his replacement - former Fitzroy forward Ross Lyon who had been one of Paul Roos' assistant coaches at Sydney over the past two years.
Fellow Sydney assistant coach John Longmire had been the early favourite to get the job ahead of Bulldogs' assistant coach Chris Bond and Collingwood assistant coach guy McKenna before the low-profile Lyon emerged late to win the position.
Lyon was one of the toughest players of his era and played under some of the game's most respected coaches in Robert Walls, David Parkin and Robert Shaw before also working alongside Parkin and Walls as an assistant coach as well as with the premiership coaches of the past two years in Roos and Worsfold, whom he worked alongside while the pair were assistant coaches at Carlton.
The Saints were rarely out of the news in 2006 with the club also involved in the most controversial incident of the season - "Sirengate" against Fremantle in Launceston in round five.
The match ended in a draw after play had been allowed to continue for about 15 seconds after the final siren sounded, when the field umpires failed to hear the siren with the Dockers' leading by a point.
During that time St Kilda's Steven Baker kicked a behind to tie the scores and then had the chance to win the game, when the umpires gave him another kick after ruling he had been felled late after kicking the original match-tying behind.
With irate Dockers' coach Chris Connolly and Dockers' officials storming onto the ground, Baker missed again and the match again ended in a draw.
The Dockers' immediately lodged a complaint and three days later the AFL Commission overturned the result of the game and awarded the Dockers a one point win, ruling that Fremantle had been in front when the game should have ended and that the umpires only failed to hear the siren because the timekeeper had erred by not continuing to sound the siren until the field umpires had acknowledged it and ended the match.
The result would prove to be a turning point in Fremantle's troubled history and the Dockers would go on to finish in the top four for the first time as well as win their first ever final.
While Fremantle were the surprise packets of the season, Geelong were the biggest disappointments after winning the NAB Cup - their first senior trophy in 43 years - and then their first two games by a total of 146 points to assume premiership favouritism.
But seven losses in their next eight matches killed their season and led to speculation about the future of Thompson, who has been in charge since 2000.
While Thompson survived a review of the club's football operations by chief executive Brian Cook at season's end, the same review resulted in football operations manager Gary Davidson being replaced by his Collingwood equivalent Neil Balme while assistant coach Andy Lovell was axed and injury-prone skipper Steven King was replaced by Tom Harley.
But when the Cats' pre-season training began, Thompson made it clear that while he supported Cook's decision he was not happy about the way the club went about the review.
"I think the whole process was pretty crappy to be honest, I didn't really approve of it," Thompson said.
"I was lucky it fell my way and we sorted a few things out, but as a club I think we've still got a fair bit of work to do."
The Cats' also had the dramas surrounding the sacking of fitness coach Loris Bertolacci, who was then accused by the club of providing confidential information about the Cats to rival clubs, while late in the season the club saw young defender Tom Lonergan put into an induced coma after he lost a kidney after being crunched heavily in a marking contest against Melbourne in round 21.
But that story had a happy ending with Lonergan recovering and winning a place on the club's rookie list for 2007.
However Geelong's problems paled in comparison to Carlton's as the Blues continued to plumb depths that were unimaginable just a few years ago.
Not only did the club record its third wooden spoon in five years but the club's finances - which have never recovered from the near $1 million fine for salary cap breaches in 2002 - continued to struggle with the Blues' revealing they were $6 million in debt.
The AFL then announced it would give the Blues' a $1.5 million interest-free loan on the condition the club met specific financial criteria.
But the club remained troubled at board level with tension between president Graham Smorgon, who took over this year from Ian Collins, and several other board members with speculation at year's end that two directors in Lauraine Diggins and John Valmorbida would be replaced.
Even worse there was tension between the board and coach Denis Pagan after the Blues' board tried to remove Pagan, in favour of assistant coach Barry Mitchell, before then doing a backflip and sticking with Pagan, who is contracted until the end of 2008.
Mitchell also remained in the club and just as things appearing to be quietening down at Carlton, Pagan revealed in December that he had been overruled by the board in his bid to recruit former Richmond and Essendon badboy Ty Zantuck in the NAB AFL pre-season draft in order to boost the Blues' struggling defence.
The Blues instead chose former Magpie Cameron Cloke with Smorgon denying the board had overruled Pagan's preferred choice.
All the while there was continued speculation of a challenge to Smorgon's board with former player Fraser Brown a prominent critic as the Blues showed no signs of returning to the stability that made them the competition's most successful club up until 1999.
But the problems of some clubs were not the only issues that dominated AFL headlines in 2006.
The saga over just which television networks would broadcast football in 2007 dragged on all year after Channels Seven and Ten won the rights for the next five years back in January by matching Nine and Foxtel's $780 million bid - a huge increase on the $500 million that Nine, Ten and Foxtel paid from 2002-2006.
Seven and Ten had hoped to on-sell some games to Foxtel, the pay TV provider which showed three live games a week in the past five years, to recoup some of their huge outlay but the three parties were unable to come to an agreement despite on-going discussions throughout the entire year.
That left Seven and Ten having to go it alone by showing four games each round next season - including up against each other on Saturday nights.
But while that was not Seven and Ten's preferred outcome, it represented a huge win for football fans - who will now see every game on free-to-air television and no longer have to pay to watch their teams on Pay-TV. Ten won the coin toss, which means it will get to show the 2007, 2009 and 2011 Grand Finals. Seven will show 2008 and 2010.
The players and the 16 clubs were the other big winners from the new television deal with the players winning a 25 per cent pay increase over the next five years.
Under a new deal between the AFL and the AFL Players' Association, the total player payments figure for each club will rise by 7.3 percent in 2007, a further seven percent in 2008 - followed by increases of 3.5, 3.3 and 3.3 per cent in the years 2009-2011.
The clubs were also handed a total of $650 million over the five year period from the deal but AFL chief executive Andrew Demetriou immediately warned that struggling club's should not see the extra revenue as "their saviour" as some Victorian clubs in particular continued to struggle financially.
As a result Victorian clubs continued to sell games interstate with the Kangaroos announcing they would shift their home away from home from Canberra to the Gold Coast after signing a deal to play up to ten games at Carrara - the former home of the Brisbane Bears - over the next three years.
The Bulldogs and Melbourne will instead play one "home" game in Canberra next year while the Dogs will also continue playing one "home" game in Darwin.
However St Kilda pulled out of its Tasmanian experiment with Hawthorn instead increasing its commitment to Launceston's Aurora Stadium, where it has played 12 home games since 2001, by agreeing to play four home games there for the next five seasons as part of a new $15 million sponsorship agreement with the Tasmanian Government.
But the Hawks, just like the Kangaroos and Bulldogs, insisted they will always remain a Victorian based club.
The year also saw an attempt by newspapers to publish the names of three AFL players that had twice tested positive to illicit drugs but the AFL successfully sought a Supreme Court order to keep the names of the players surpressed - arguing that publication of the names would threaten the league's drug code which aims to counsel and treat players for drug abuse in confidence.
The league's new kick-in rule, which was bought in amid much outcry at the start of the season, proved a success while by year's end the AFL announced a crackdown on head-high bumps to provide greater protection for players with their heads over the ball and minimise the chances of players suffering serious spinal injuries.
The fully-renovated MCG also opened to great acclaim with the AFL enjoying its second highest attended home and away season on record in 2006 with a total of 6,204,056 attending the 176 matches, behind only last year's total of 6,283,788.
