AMD has had a few cycles of it over their history.
There was a stretch of bleak years where Adobe's reputation had become quite bad (not least of which was their software becoming one of the biggest security risks).
Microsoft for the better part of a decade had burned its reputation, between some really bad security problems and Vista. If you had polled most techies about Microsoft in the midst of Vista, the resounding view would have been that they had a dim future. It has taken many years to recover some of that lost reputation.
Electronic Arts is a company that has managed to remain quite successful over time despite becoming belligerently infamous at times for their product quality and corporate behavior. They had some very bad financial performance years, but have somehow managed to recover from that despite not really improving their reputation. Probably the benefits of being one of the few companies left standing capable of putting out hyper expensive tier one titles.
Myspace.
Hewlett-Packard.
Symantec.