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I have a Server 2008 R2 server. Is it a good idea to make this a Hyper-V root partition, and install SQL Server 2008? What issues might I run in to?

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Sure.

I typically have almost nothing running in the root of my hyper-V servers. I like to make them as simple as possible.

I also have several SQL 2008 servers in child partitions. Have to admit that the SQL servers are NOT overloaded...at all. Would just be careful with how much you load up the SQL boxes. Check out brent ozar's blog for some overview kind of links to SQL on Hyper-V.

http://www.brentozar.com/

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At the end this is not a hyper-v problem. If yuo have a busy server then sharing the hardware just dont work - because most of the resources go to one machine anyway.The usual caveats apply - Sql Serer in higher usages wants carefully layed out disc setups, so a "typical" hyper-v server wont work (lots of ram, some cpu, shitty disc subsystem). The requirement to plan your IO budgets does not magically disappear for SQL Server just because you use it on a Hyper-V child. –  TomTom Jan 12 '12 at 8:26

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