Presuming the logical course that the Oregon Ducks and the Stanford Cardinal do not lose any other games outside of the one they play in Palo Alto, it wouldn't be a huge surprise to see these two Pac-12 teams hit the BCS this season. In fact, it should be expected.
It should be noted that Stanford winning out does not necessarily put them in the BCS title game. Although Stanford should pass by Alabama with a win on Saturday, there's a huge gap for the Cardinal to overcome to catch up to #1 LSU and #2 Oklahoma State. Both of those teams appear to control their own destinies. Presuming all three schools win out, Stanford would likely earn the Rose Bowl bid.
A two-loss Oregon might seem doomed in this scenario, but remember that their two losses would be to two of the top three teams in the country. The Ducks wouldn't be heavily punished for their increasingly difficult strength of schedule, and would probably not drop out of the top 14 of the BCS rankings. They would have to fight for one of four at-large bids. One would probably go to Boise State presuming an undefeated season, another would probably go to the SEC runner-up (likely Alabama), and another to the Big 12 runner-up (Oklahoma/Oklahoma State loser). Whether the Fiesta Bowl (the only other West Coast BCS bowl) would want to select Oregon over another conference (the Big 10 runnerup?) remains a bit of a mystery at this point.
If Oregon loses on Saturday, they are probably rooting for Stanford to win out and an upset somewhere among the top two so the Cardinal end up in the BCS title game. That'll free up the Rose Bowl bid, who will want to preserve the Big Ten-Pac-12 traditional matchup. The non-AQ rule that forced the Rose Bowl to select TCU no longer applies, so the Ducks would end up back in the title game.
Things get a little more complicated if Oregon beats Stanford. The Ducks road to the BCS title game is far more perilous than Stanford's, as a lot of teams ahead of them would have to lose once (and even that's not a guarantee to bring the Ducks to New Orleans)
Stanford's fanbase has been challenged at showing up for their team for a bowl appearance. The Cardinal were only selected for a BCS bowl because they were among the top four schools in the overall rankings last season, and they were chosen by the bowl with last dibs on the playground. And thus Stanford pounded Virginia Tech in a half-empty stadium in Miami with only a few hundred Cardinal supporters in attendance.
The BCS is all about ticket sales, and there just won't be any appeal for a Cardinal team that doesn't bring any other fans to the stadium. The only hope is that the Andrew Luck buzz is enough to carry a local showing by local fans in need of a quarterback (Miami and Phoenix come to mind...). Stanford would have to hope just as much as Oregon for chaos, and hope they somehow get to the Rose Bowl as a result.
Basically, both teams can still gain a nice consolation prize if they lose. But they'd need a lot more to get there. Honestly, they'd both be better off winning.