Starting pay is extremely low for a tech company, even considering the area. If you take such a low salary, you will find it difficult to move on and command the salary you should receive in the future.
That would be fine, if it were not for the pathetic raises also. My annual raises usually BARELY beat cost of living. And one year, they even blamed the economy and had a "salary freeze". I am sure that did not also apply to upper management. I graduated college while still working for them, and asked for a raise. The bureaucracy at Applied is so bad, this process was like pulling teeth. In the end, I did not get at all close to what I deserved, considering what I put into the company. Ultimately, I had to jump ship to another company because I could see that staying at Applied would get me nowhere in my career, salary-wise.
Bonuses were a joke too. $500 or $1000 was typical.
Management is constantly changing. I had probably 4 different managers in the 5 years I was there. This is partly due to high turnover, partly due to new ownership. Management only cares about the bottom line (the company is owned by a venture capital firm -- their whole purpose is to maximize profits).
I had to constantly track my time spent, in 15 minute intervals. I cannot complain enough about how much of an annoyance this is. It impedes and interrupts actual work, and is overall a big waste of time.
The cubicles are cramped. Most of them (for developers) are in the basement and windowless.
I was not allowed the flexibility to work from home. I believe this has changed since I left though, at least for some employees, 1 day per week.
The 401k plan had poor fund options (high expense ratios).
Medical plan was not fully paid for by the company.
Vacation time was only 2 weeks. You had to put in 5 years to get 3 weeks.
But despite all of those complaints, I would have stayed if it were not for the laughably low pay and raises. Ultimately, we all work to earn a paycheck that fairly compensates me for my skills and abilities. That was never going to happen at Applied.