The end of the Yamaha-backed effort does not necessarily mean that there will be no Yamahas on the grid in 2012. When Yamaha announced they would be pulling out of World Supersport at the end of 2009, they made it clear that they were open to supplying bikes and support to a good team. That did not happen in 2010, but Yamaha have provided some backing for the current ParkinGO Yamaha World Supersport team, and have been rewarded for their pains as Chaz Davies leads the WSS championship by 42 points with 4 races left to go. The same construction could save Yamaha's involvement in World Superbikes, if Yamaha can find the right team to work with. Their involvement would, however, be scaled back severely.

I think the sooner we have no factory involvement in WSBK the better. A lot of journos in twitterdom are lamenting the fact that Yamaha are pulling out, but part of me wants BMW and Aprilia to do the same so the series can return to its roots, where privateer teams can cost effectively campaign production bikes, therefore creating a clear distinction between it and GP racing.
Let's get all the factory teams out of superbikes, dumb down the regs to Superstock level and let the privateers return to ruling the roost. It will never match the lustre of MotoGP - but WSBK never had a chance of matching that in any case - yet it should offer (relatively) affordable, production based racing that is sustainable in the long run.
For far too long WSBK and MotoGP were on a collision course and if all the factories leave WSBK it might save the FIM having to make some hard calls in the near future.

WSBK should be devoid of factory teams b/c all parts (racing or stock) should be sold on the open market. If every part is sold on the open market, and the tuning rules are friendly to privateer teams, no factory squads are required. Believe it or not, the MSMA actually knew this to be the case going into the 1000cc era. Superbikes must be halo products that represent a larger lineup of sportbikes. Surprisingly, it was the Flamminis who understood that the superbike brand couldn't be diluted for profit.
Predictably, as with so many things in motorcycling, we got the worst of both worlds--prototype racing parts, no homologation specials, and diluted superbike brands. The arrangement hasn't generated any positive long term consequences.
Though the situation is ugly in WSBK, Superstock regulations will not improve anything. Superstock further dilutes SBKs, and it encourages the manufacturers to equip road bikes with race equipment. Sounds sexy, but it's just a waste of money.
Imo, they have to go back to homologation specials. It fixes damn near every problem in the superbike racing industry, but it can't happen until they write some really good homologation papers b/c WSBK can't revisit some of the 750cc-era homologation problems. Homologation papers have to stipulate things like valve-count per cylinder, maximum bore measurements, static compression ratio, type of cam drive, number of fuel injectors, max fuel pressure, number of electronics sensors, function of electronics sensors, and most importantly a rev limit and a single displacement for all competitors. The rulebook would then be simplified to allow bolt-ons, basic chassis mods, and simple engine tuning like fuel mapping and cam modifications.
Solves almost every problem, imo. SBKs are production bikes again. Electronics are dealt with. National series have almost identical rules and bikes. Superbike is no longer a diluted concept. Also, pursue other concepts like engine scaling (750cc triple supersports, 500cc supertwins), and motorcycling might be onto something that pulls the industry out of its funk. With the Western debt crisis, the yen ain't getting any cheaper. If they want profits in Europe and the US, it's time to go upmarket, and drastically reduce expenses in the middleweight and entry-level sportbike segments. No time to waste.

Yamaha will continue the availability of road racing kit parts, known as YEC Racing kit parts, for its R1 and R6 production models for private teams entering at all racing levels.