There's smoke, but is there fire?

Facts

1. The complaints are all fairly localized: businesses in Oakland, and the Yelp Elite program in Chicago.
2. CEO Jeremy Stoppelman denies that manipulating reviews to benefit advertisers is Yelp policy, and can cite customer and staff testimonials to back that up.
3. Numerous Yelp customers in other places have good things to say about Yelp's customer service and integrity.
4. Yelp competes with the restaurant review sections of newspapers and weeklies.
5. The newspapers (SF Chronicle, Chicago Tribune) and weeklies (East Bay Express) have been the ones covering the "Yelp controversy".  In the case of the Chronicle, even before it existed.
6. Yelp is not profitable, and has already had its fourth round of funding a year ago.

Conclusions

The Chronicle, Tribune, and Express have motivation to uncover as many tales of Yelp wrongdoing as they can find.  Thus we can conclude that the incidents cited to date are the majority of all of the incidents which have happened.

Yelp is probably nearly out of money.  As a result, Stoppelman is probably powerless to fire any sales staff who are "good producers".

Final Answer

What we have here is not a general "Yelp Mafia" but rather 2 or 3 unscrupulous salespeople who have been using dishonest pitches to try to make more sales.  Because Yelp is desperate for cash, they can't fire these salespeople even though they're hurting Yelp's credibility.  However, these incidents do not affect Yelp reviews in general except to remind everyone of Yelp's limitations: astroturfing, anonymous attacks and the sponsored default ordering of reviews.

Corollaries

Yelp is almost broke and may soon be offline.  Or, worse, bought by Microsoft and destroyed the way CitySearch was.

Also, based on the fates of Yelp!, CitySearch, and Sidewalk.com, it may be impossible for a review site, no matter how popular, to return a VC-worth profit.  I know I wouldn't invest in one at this point.