Just a few thoughts, necessarily general because you didn't specify any performance parameters or any information on where the nameserver will be placed in your network architecture.

I would start by considering the rest of your infrastructure and method of operations. If you're a mostly windows shop, then there's a benefit to using Windows tools, since they'll be more familiar to your staff, and likely inter-operate better. Also, if you like GUIs, the Windows DNS server has one, and as far as I know, BIND doesn't, although there are third party products that can give you one.

As far as security goes, I personally think that both BIND and Windows DNS are relatively robust, but I haven't checked recently. I would probably do some research, looking at how frequently, and of what severity, each had reported security issues, say over the last 2-3 years, and how quickly patches were produced.

Features: I think the feature sets are comparable, but depending on your thoughts on the management part above, you might find that you're more comfortable configuring Windows to do Dynamic DNS updates, say, than doing the same with BIND. It really depends on what features you're looking for - Dynamic DNS, DNSSEC, etc.

Performance - without a good understanding of what you'll want to get out of your DNS server for performance, it's hard to say. I have generally found that it often takes more hardware to run a high-capacity DNS server on Windows than on Linux. But then again, I know how to tune Linux machines, and my skills in that area for Windows are less well developed.

It's quite easy to generate a lot of DNS traffic on a test network. If performance is really a concern, I generally find that actual testing seems to be the best way to determine that.