I just completely overhauled my company's data storage - that was a job and a half! Not just GIS datasets either, it was the whole shebang. The most irritating and tedious part of it was updating links, sources and hyperlinks in everything GIS-related, which took almost as long as the workover. But when circumstances allow, such as reorganising datasets you have at home, there can be a better way...
The trick is to do as little work as possible. Decide on your new naming convention and filing system and document it, storing it at the root level or stuck on your noticeboard for ease of reference and to drum it into your head. Then change all the datasets and folders you can stomach (in my case about four

) to the new style. Then leave the rest.
Whenever you acquire a new dataset, store it in the new fashion. Whenever you update or replace an old dataset, store it in the new fashion. Over time your data will naturally migrate to the spiffy new system. It's the lazy, easy way to do it. Maybe I should call it the
Sunday Mornin' method. The beauty of it is that you can start off with a big burst of organisational energy and then let it continue almost unaided when you get fed up. I think this is how a lot of people operate anyway, but it's surprisingly effective if you apply it with gusto and change the less frequently updated data first.
Emily