In order to come up with really great questions to ask in the interview, you'll need to do some research about the company, the company culture, the industries the company is in, and where that industry will be in the next five years.
The more you research about the company, the more basic questions you'll answer on your own. But most importantly, the more questions you answer on your own, the more advanced, targeted questions you'll think of that only a member of the company can answer.
If you ask these questions, you'll demonstrate that you're more than just another mindless coding-drone. Your future employer wants to hire someone who will be capable of growing into other roles in the organization, and this involves the ability to think about the goals of the business as well.
Remember, people love to talk about themselves. So if you can get your potential employer to talk about the interesting future direction of the business and actually have a conversation about it, the interviewers will likely like you and respect you. These attributes may help differentiate you from an equally qualified technical candidate, and they could even differentiate you from a candidate with more technical skills than you!
Additionally, ask questions specific to your career growth. Ask questions that imply you're looking to stick around for awhile and that you are really interested in being a part of the organization for the next few years.
What options for growth do I have as an SDET in this organization? I see myself moving into a management position in the next 5 years, and was wondering what the career path looks like?
This question could either preempt the "Where do you see yourself in 5 years question?", or it could be the answer to that question. By asking a question yourself, it helps you take control of the conversation. If you're in control, you're likely to make a better impression on the interviewer that you're a leader and not just another follower.
If you're building software for car dealerships: I saw some research that said that by the year 2015, one in five cars will be purchased online through the mobile network. Does this company have any plans to move into mobile development? If so, what type of mobile testing strategy have you considered?
This is a great, industry-specific question that demonstrates you've done your homework. It also relates to your field of testing and demonstrates that you're interested in the company's future. It's not a question that you can necessarily answer yourself just by Googling the company. Finally, this question could spark an interesting conversation where you can make some suggestions for how to approach the problem in the future.
Example Bad Questions:
How many employees work here?
Only ask if you've researched it and cannot find the answer. For companies like Google and Microsoft, and other public companies, this information is available in their public annual reports.
Do you use JMeter/Selenium/HTMLUnit/INSERT TESTING TOOL HERE?
In general, try to stay away from questions that involve simple one-liner answers. Instead, look for questions that incite conversation, such as the "Where will we be in 5 years question in terms of mobile testing".
Remember, employers are looking for a wide variety of skillsets, and technical skills are but one of many that they consider important. Employers want to hire people who can think for themselves and who can get out of their own way.