This is a great question, in fact it needs more upvotes.
I was so interested in this myself that I wasn't going to stop at anything to get a good answer. Sadly, small research didn't get me the answers I was after so eventually I spent 14 hours reviewing the reports of every Grand Prix since 1950. To the date of this answer there have been 864 of them, which is why it took so long:
Grand Prix in which the fastest qualifer didn't start from pole
1955 Indianapolis GP - May 30, 1955.
Jack McGrath set the fastest qualifying speed but actually started in grid position 3, on the outside of the track. Jerry Hoyt started in pole as he was one of only two drivers to complete a qualifying event on "Pole Day" due to strong winds and the threat of heavy rain. Hoyt was actually only the 8th fastest in the field and his speed (140.045mph) is the record slowest ranked pole speed.
1994 Monaco GP - May 15, 1994.
This was the first GP to follow the deaths of Ayrton Senna and Roland Ratzenberger at the season's previous Grand Prix at San Marino.
Whilst Michael Schumacher did start at pole position and is officially documented as such, grid places 1 and 2 were left unoccupied and painted with the flags of Senna and Ratzenberger's respective nations as a mark of respect.
1996 French GP - June 30, 1996
Michael Schumacher qualified with the fastest lap, earning him pole position for this race. However, Schumacher's engine failed during the formation lap at Magny Cours and did not take his place on the grid.
1998 Japanese GP - November 1, 1998
Schumacher was involved again here, this time stalling from his hard-earned (1/10th of a second faster) pole position. As a result of this he was sent to the back of the grid. The race started successfully on this, the third, attempt after Jarno Trulli had stalled his car on the first attempt.
2001 Monaco GP - May 27, 2001
David Coulthard was sitting happily in pole position but his McLaren failed to pull away for the formation lap. His team managed to get him moving eventually but by this time he was resigned to starting from the back of the grid.
2005 US GP - June 19, 2005
This is the one they called "IndyGate". Jarno Trulli was fastest qualifier and therefore in pole position. However, due to safety concerns regarding the Michelin tyres, all drivers of vehicles with these tyres retired to the pits during the formation lap.
Only six cars started the race with drivers in grid places 5, 7, 17, 19, 18 & 20.
2005 Italian GP - September 4, 2005
Kimi Räikkönen qualified with the fastest time but was given a 10-place grid penalty for changing his engine. Juan Pablo Montoya took up pole position as a result.
2007 Hungarian GP - September 4, 2005
Fernando Alonso recorded the fastest time in qualifying but a stewards' inquiry before the race adjudged Alonso to have impeded Lewis Hamilton during Q3. Alonso was subsequently relegated 5 places on the starting grid, moving Hamilton up to pole.
2012 Spanish GP - May 13, 2012
In this event, Lewis Hamilton was excluded from the qualifying results due to having insufficient fuel to return to the pits. As a result, Hamilton had to start the race from the very back of the grid.
2012 Monaco GP - May 27, 2012
The fastest qualifier at Monaco was Michael Schumacher. However, Schumacher was carrying a 5-grid penalty from the previous race in Spain for causing an avoidable collision with Bruno Senna, thus moving him back in the grid.
and it nearly happened in:
1990 Japanese GP
Ayrton Senna had secured pole position but was unhappy that pole was situated on the side of the track which was not on the racing line. Senna requested that he be moved and the stewards agreed, only for the FISA president to overrule the decision, meaning Senna started in pole at the original location.
And to close, you ask:
There is a reason for the question as the Fantasy F1 game I run gives the pole-sitter bonus points but I am not sure what to do in this kind of situation!
You'll have to decide! Perhaps give the bonus for fastest qualifier instead of pole position?
You can see my spreadsheet with all the pole positions since 1950 here.