I've tried various methods, but the one that has proved most successful for me is to edit the text in Word (making proper use of styles etc) and then use Atlantis to generate the ePub file. You could use Atlantis for everything, but I find Word 2007 easier to use for editing (mostly because I'm used to it and I have it anyway). The $35 for Atlantis is very reasonable for what it offers. The advantage to this is that I can edit the text in a word processor and don't have to guess what it will look like or fiddle with xml to set things up properly.
I have access to inDesign CS4 and have tried it for ePubs, and frankly it's inferior to Atlantis - you need to split the book into separate documents yourself in order to ensure that it doesn't go over the mobileADE 300k limit, which is just the sort of extra hassle I can do without. inDesign does offer more flexibility with ToC generation, has options for image manipulation and makes it easy to embed fonts in the ePub, but none of these justify the extra effort involved unless you have special needs.
I'm sure you can get excellent results converting rtf files in calibre as well, which has the benefit of being free. For best results you'll probably want to tweak the css settings and XPath options for the ToC etc. There are also a few free add-ons to Word floating around that might be worth checking out, though they tend to enforce their own particular notions and can be fiddly (hard to moan when they're free though).
One thing you need to realise is that PDFs are a real pain to convert. Very few are fully tagged, meaning that you need to scan through the text to correct broken paragraphs and incorrectly inserted line breaks or hyphens (I use a Word wildcard search for paragraphs, Find: ([!."\?\!\)])^13 Replace:\1 though you still need to check each instance). Each document will offer its own variation of the particular problems you can run into. I'm afraid there is no 1-click solution, converting a PDF can easily take a couple of hours, or much more depending on how much you need to reconform the text. A lot depends on how much variation there is in your text and how much you want to preserve that in the finished item. There are various options for saving the PDF as a docx file for editing. I happen to use Nuance PDF Converter, which generally does a decent job of stripping out headers and footers, though it can still trip up at times.