The NVIDIA GeForce GT 120 or the ATI X1300 board that Apple offers within (whichever) Xserve box is the usual choice.
See [messageID=9219032|http://discussions.apple.com/thread.jspa?messageID=9219032] for a recent discussion of this.
The Nehalem 2009 Xserve box has two PCIe x16 slots. One long slot, one shorter. Most high-end graphics controllers want an x32 slot for full speed.
Plan on an acoustical rack-mount cabinet, too, if you're planning on working next to the box. Or go for the Mac Pro, which has higher-end graphics, and is a quieter box.