Lately I have been noticing a slowdown when I activate Spotlight. My searches would not begin for a few moments, and then would take a moment to complete.
I thought it was because of my two 500GB internal hard drives, but I found something while browsing my Energy Saver Preferences, a 'Put the hard disk(s) when possible' checkbox.
After unchecking the box, I've have a noticeable speed increase on my searches. Startup searches as well as complete indexes take a fraction of the time they used to.
Seems like a rather simple fix, but it was driving me crazy for the past few months.
[kirkmc adds: If one of the drives is asleep, then Spotlight searches will certainly take longer as the drive has to start spinning before Spotlight can access its index. As to why this would speed up indexing, however, I don't know. If you write to the drive, Spotlight indexes new files immediately, and the drive will be spinning when you write files.]
Mac OS X Hints
http://hints.macworld.com/article.php?story=20060423213955658