The D5000 doesn't have an AF motor for older AF-D's so I would suggest a Tamron 90 Macro with built-in motor ($399 at B&H after rebate), or if you want a Nikon, there's the new 85mm 3.5 DX VR lens for $530. (honestly - get the Tamron)
and since you said you're willing to manual focus, I say go to KEH.com and hunt a BGN or EX copy of either the 60mm or 105mm Micro Nikkor which is an AF-D. They go for around $350-400 used and will work fine with your D5000, minus the autofocus.