Another option (for mogui in particular) is to use Stingo's Word macro (available in the conversions section of you local MobileRead Wiki.) Even if you don't have Word installed the VB code can be easily adapted to the free OpenOffice word processor. It fixes those pesky hard returns at the end of each line.
Also, I've imported text based PDF files directly into BookDesigner and and then clicked on Make Sony eBook with very good results. I wouldn't distribute the files but they are a lot like the PDFs that AvidReader described.