The first time was after the 2008 season. Smith experienced shoulder injuries that wiped out most of 2007 and all of 2008. However, Smith accepted a huge pay cut to remain with the 49ers in 2009.
The second time Smith appeared destined to leave the 49ers was following the 2010 season. He was clearly ready for a new chapter in his life. But, then, Jim Harbaugh came along and an agreement was reached. Both sides came to the conclusion that it made sense for Smith to remain with the 49ers on a one-year deal.
(Last offseason, there was always the sense Smith would return as a free agent even throughout the whole Peyton Manning saga.)
But now that Harbaugh has made the move to go with second-year quarterback Colin Kaepernick as the 49ers' starter, it seems Smith is back in that old familiar position of uncertainty.
Smith signed a three-year, $24 million contract with the 49ers in the offseason. Because that contract is so reasonable, it gives the 49ers some options.
If Smith is on the 49ers' roster on April 1, 2013, his entire $7.5 million base salary becomes fully guaranteed.
Obviously, a $7.5 million salary for a backup quarterback does not seem realistic when the presumptive starter, Kaepernick, is scheduled to make $740,000 in base pay.
If the 49ers were to get rid of Smith's base salary, they could then use that money to tender safety Dashon Goldson at the franchise tag of $7.45 million.
Smith is the 20th-highest-paid quarterback in the league (see table below), which could make him an attractive option for some quarterback-needy team to acquire in a trade -- probably for a 2014 draft pick.
Smith is scheduled for a base salary of $7.5 million in both 2013 and 2014.
If the 49ers simply released Smith before April 1, they would still owe him $1 million. So it would help the 49ers on the salary cap, as well as enable the organization to accumulate a future draft pick, if they could get something for Smith via an offseason trade.
Here's how Smith's average salary per season ranks among other quarterbacks in the NFL (with years the deals span):
Average QB salaries per year
1. Drew Brees $20 million (2012-2016)
2. Peyton Manning $19.2 million (2012-'16)
3. Tom Brady $18 million (2010-'14)
4. Eli Manning $16.25 (2009-'15)
5. Michael Vick $16 million (2011-'16)
6. Matt Schaub $15.5 million (2012-'16)
7. Philip Rivers $15.3 million (2009-'15)
8. Jay Cutler $14.67 (2009-'13)
9. Ben Roethlisberger $14.67 million (2011-'15)
10. Mark Sanchez $13.49 (2012-'16)
11. Sam Bradford $13 million (2012-'15)
12. Aaron Rodgers $12.7 million (2008-'14)
13. Kevin Kolb $12.42 million (2011-'16)
14. Matthew Stafford $12.25 million (2012-'15)
15. Tony Romo $11.25 million (2011-'16)
16. Matt Ryan $11.25 million (2008-'13)
17. Carson Palmer $10.75 (2012-'16)
18. Ryan Fitzpatrick $9.83 million (2011-'17)
19. Matt Cassel $9.67 million (2009-'14)
20. Alex Smith $8 million (2012-'14)
21. Matt Hasselbeck $6.67 million (2011-'13)
22. Matt Flynn $6.5 million (2012-'14)
23. Andrew Luck $5.53 million (2012-2015)
24. Cam Newton $5.5 million (2011-'14)
25. Robert Griffin $5.28 million (2012-'15)
26. Josh Freeman $5.24 million (2009-'13)
27. Joe Flacco $4.76 million (2008-'12)
45. Colin Kaepernick $1.28 million (2011-'14)
(NFL Players Association sources)