Like many software product companies, we spent an exorbitant amount of money in 2008 developing our product. I’ve heard that there are federal R&D tax credits available ("Section 41 Credit"), but our CPA does not specialize in this area, and advised that we hire a consultant who can evaluate whether our activities would qualify.
Have you had any experience in R&D credits for software product development?
I have filed SR&ED tax credit applications for the past 8+ years. This is a Canadian program; I suspect you are talking about a program in the US?
In Canada one of the best things you can do is go through a pre-qualification process, where you have both a financial and technical consultant come in and evaluate your application. There are many consultants here who specialize in SR&ED apps but I prefer to handle ours directly. My understanding is that most businesses opt to use a consultant, who tend to charge a percentage fee on the annual claim amount.
We've built our own time reporting / project management system to synchronize with SR&ED reporting. It makes it fairly easy to separate standard vs. R&D research at the end of the year and we also aim to do an internal report every quarter.
Sorry that I can't offer any specific advice for companies outside Canada.