I have had great success using Calibre, but not without some trial and error. I have found that using the Kindle DX output format works well in iBooks. If you just drag and drop using stock output, there will be formatting errors.
Thanks for that suggestion...I've been using the default. I hope they're working on an iPad specific format.
In the Calibre forums, the guy who wrote Calibre said there was no need for iPad specific output. He said to use the Sony reader output.
I'll give it a shot when I get home, I've been using default and it gives me a ton of blank pages and the font is to small to read. I've been using Goodreader and like how I can zoom with it. I'll try both the Sony and the Kindle settings to see if it gives me better results.