Personally I've played with CFD a little but generally don't depend on the tool(s) for the design process. Even some of the better codes have sufficient limitations to make the results less than useful. Only when particular procedures are in place that assure that the modeling environment and initial assumptions are accurate, can the results be representative of the eventual product. This either takes a lot of experience with a particualr product or, a combination of that and a very pricey system.

Several years back I was in a meeting with a design engineer who specalizes in CFD for United Technologies (Pratt and Whitney). When the subject of CFD for up front design came up, he smirked and indicated that as far as usefuleness is concerned, in his industry the rather pretty pictures are commonly refered to as "clown puke". In other words, they are pretty, make for good presentations, impress the non-technical crowd but in reality, unless there is a verifiable baseline in place, the results shouldn't be depended upon for a high level of accuracy.

So, to answer your question, I do use CFD from time to time but we actually subcontract the work out to an organization (AMI - Analytical Methods, Inc.) that specializes in this analysis and has the procedures in place to do it right. The two primary tools we use are VLAERO and VSAERO. The first is for derivation of the neutral points and control authority while the second is for performance prediction and to assure ourselves that we're not running into any flow problems (interfearance, flow separation, etc.).

All up front work however is purely based on experience and our own in-house software. The CFD is used only for verification and applications where the upper end of the performance envelope is significantly over 300 mph. Below that, the extra tiny bit of information you gain is usually not worth the expense.