Family Tree Maker was the first (as in back in the days of windows 3.1) and is still the best in my book. It saves all data in the universal .GED format that can be read by all other geneology prgrams as well as PHP and .NET scripts to create dynamic web based representations of what you compile in the program. The newest version runs for about 50.00 but you may be able to pull a student discount.
It's made by Borland and thus has my respect for Borlands tech support as well.
My family uses it and where able to trade the data with other families with similar surnames. There are even entire communities of people trading and compiling the .GED data of everyone who submits to create the tree of the entire US population of European descent (it's a stalled project in the last year though)
But yes, it supports multipule wives as long as you can provide the death dates of the wives, as well as a host of add in scripts that support things like Titleling families, genetic lines, or indiviguals. (there's even a bastard child modue floating on the internet somewhere
)
Hope that helps.