This question was previously asked with the qualifier of Sitecore 6.x.
Since Sitecore 7.0 is out and widely used my team and I are in need of a new answer and debate to this question.
What would be the best way I can rebuild a custom index in Sitecore 7.0 Content Delivery?
Edit: (More Info) I do not have access to the code being developed. I run about 320 different websites across multiple Sitecore Instances most sites have their own Lucene Indexes.