There are plenty of free application development tools, including the Express ones from Microsoft. The development cost is swamped by the salary cost, so I don't think the cost of the tools matters.

The big question for me is the product lifetime. If a tool is successful, I wouldn't be surprised if it's still used in 5 or 10 years time. In that case your decision should way up the maintenance costs. Microsoft will force you to port to a new version of Windows and a new toolset during that time (been there, got the scars), but at least there will be plenty of developers with the experience to do it. Linux doesn't tend to go through these big upheavals, so it's a good choice for future proofing.

Personally I prefer to write applications in Java. It's multiplatform and has a good user base and developer community.