1) Do you mainly use TR for work, personal, or both?
For the benefit of "Stress Free" in productivity only kicks in when you cover 100% of your life.
2) Do you use just one data file or do you separate them?
I use one data file; however, to do that you need a reliable system for syncing and accessing.
Ideally it would be running on a Ubiquitous Capture Tool, which would go every where.
3) What are you contexts? If the list is too long then some primary examples would suffice.
Essentially:
Work
Home
Moving
Phone
I suspect each person has some more personal contexts ex. Gym/Studio/Garden. I started with more contexts, but have found it better to reduce the list, when possible.
I also carry a Ubiquitous capture tool to track Home and Moving items that are current. I spend a few minutes each day transferring things from my wallet to TR. While my wife loves the fact that I do GTD, she does not like me looking at the computer, when we talk.
4) What are your topics? For example do you use general topics like Work and Personal or do you have specific topics like Work - ClientName.
Topics are likely very personal
Acquire (buy, beg, borrow, or steal)
Dating
Family
Finance
Friends
Home
Vacation
Personal
Software
Themelody (my production company)
Kodak (major commitment)
For contractors, Client Name as a Topic, would definitely make sense. The Action search is great, so it will find all actions, if you include the Client name in the action/note.
5) Are your projects highly hierarchical such as Work->Clients->ClientName->ProjectName->Subproject or is it more flat? If it is more flat do you organize it some other way, perhaps with topics, or do you just not need the extra logical levels?
Both, I prefer not to have hierarchical structures, but if you have a project that will take 1000 hrs, you will want to break that up. I produce albums, and in that case I use a hierarchy
6) What screen do you spend the most time in?
Overwhelmingly: Actions. I highly recommend customizing the Actions Screens, in Tools, Options, and Action Screens. I've set up a couple of addition action screens: Phone, and Quick. It's really nice to see the few calls, or things you can do at you computer in just a few minutes.
7) What options do you use for the review actions screen? Specifically do you like to only see ASAP items mainly or do you see everything but rely on sorting or colorization to differentiate?
I mostly like to only see ASAP, and scheduled actions. For inactive and delegated, I have customized Action Screens that let me see the much longer lists only when I have additional time.

Do you leave TR open all the time? If so do you minimize it?
Yes, when I'm at a computer Thinking Rock is open 90% of the time, often minimized.
9) Do you use another system or program to record thoughts and then import them into TR? If so, what system(s)?
Sometimes a simple text editor, using the import thoughts.
I also paid for a membership, and with that you can e-mail thoughts. I find that quite useful.
10) Do you use the iCal synchronization? If so, with what program(s)?
No, but I'm interested. Currently Outlook rules my Calender world, because of corporate edict. It would be awesome to get that working, so the Today Action Screen would also include my Calender events.
11) How do you deal with things which could be done "whenever"? Are they ASAP, inactive, scheduled, etc.?
Definitely not scheduled. David Allen really pushed the idea of only schedule things that will die, if not done on that day. When I schedule actions that do not fit in that category, I often disappoint myself. So if it is important, then I make it ASAP. If it unimportant, I make it inactive. I then have my action items set up so I can see quick unimportant, low energy inactive items. So when I'm toast, I take a look. Hey maybe I should spend 15 minutes in TR forums.