I've had many jobs. In fact, I've had more jobs than nearly anyone I know. I've worked for companies that have earned various "Best Companies To Work For" awards - usually from local newspapers, and I've worked for some that have not. Should you apply for a job at a "Best Company To Work For" company?
As a hiring manager, my advice is simple. Don't put too much emphasis on these types of awards. In fact, don't put any emphasis on it. There's no reason to avoid these companies. Just ignore the "best companies" distinction.
There is evidence that even some "best companies" treat candidates poorly.
How can this be?
Many "best companies" treat the campaign to earn the award as they would any marketing endeavor. Given that these awards are almost always given out by a newspaper or magazine, it should come as no surprise that simply seeing a company listed as a best place to work doesn't make it so.
Do your own research. Long-term growth and portability, strength in the marketplace when compared to competitors in the industry, and customer feedback should each carry a greater weight than any "Best Company..." award.