Alteryx®¹⁾ is a great spatially oriented ETL tool. It allows you to do many spatial operations such as finding intersections, etc, within a very user friendly GUI environment. However, with SRC's recent move to become “Alteryx®, Inc.” the price of this tool pretty much puts it out of reach of just about anyone without very deep pockets…to the tune of nearly 6 figures for a single user one year license (at the time of writing). Especially considering that a comparable tool exists that is free and open source, GeoKettle.

Anyhow, take a look at it, it's a good tool, and maybe the license fees will come down over time. Also take a look at Pentaho Data Integration ²⁾(PDI, formerly known as Kettle), as I believe it can be easily extended to handle geospatial operations as well.

These days, I prefer to write Python code to do most of these kinds of things, because it's testable, repeatable, and reusable, and it doesn't really take that much time. I will occasionally dust off PDI if I just want a one off transform, but inevitably that one-off become something I need to do again and I find myself wishing I had written it in Python.