Dune: Chronicles of the Imperium (aka Chronically Cancelled by WotC After WOTC Brought Out LUG) had a print run of 3000, as a result of their travails.

How does that compare with today's print runs?

Who knows?

Over the years on forums, I have heard rumors of 2k initial print runs by mid-tier publishers and 10k initial print runs by WotC and WW for their non-core books.  It's certainly a pitiful joke compared to the 1990s.

As for their accuracy, I have no idea if the posters who said they had inside info about these numbers was speaking out his ass or not.

As for the bottom tier (mostly indie or OSR guys), I hear about POD orders in the low 100s.

But perhaps this isn't all bad news.  

From what I can gleam from Palladium, they have a close relationship with a local printer so they can do 1k print runs easily with little transport costs so there is no reason to stockpile lots of books in the warehouse.  Instead, they can keep the flow based on the needs of their distributors.

I hear about this from the micro-brew industry as well. Thanks to today's computerized tracking in retail outlets, the brewers can get an accurate picture of what sells where and what doesn't and can target markets accordingly.

Also, keep in mind that there are odd tax laws in the USA about back stock in warehouses. That may also be encouraging publishers to do small runs.