I use Homebase as my database program (provided free by ABE; subscription required for ISBN lookup). It allows me to upload to most of the sites I list on. On Amazon though (using the "UIEE" method) it only matches the ISBN-bearing titles, leaving 4/5 of my inventory unlisted.
Recently I started experimenting with Amazon's "Standard" upload method. This requires a tab separated text file with specifically-named columns that I created by adjusting the column titles in a Homebase export. Now all but a handful of my books are listed on Amazon and I've definitely been moving some unexpected titles for that venue.
But now when I sell a book I have to update 3 separate records (Homebase, the tabbed text file, and my eBay store). Quite a headache with a large possibility of error.
How do other people handle listing on multiple venues? I'm not willing to pay ANOTHER monthly fee--or a commission--for one of the web-based services. I've been considering building my own database in Filemaker that could create multiple uploads formats...but that's a little too ambitious at the moment.