Its tricky because (as can be seen from the parent topic) there are quite a number of competing formats at the moment and like the VHS vs Betamax war in the video market you don't want to have all your data in a suddenly defunct format.
To this end it would advisable to store your data in a more general format and export it to the desired format. Except for the high end solutions not all the formats are easily available so you still might need to look into the various subsections of the parent of this FAQ as there are plenty o useful devices to make exporting easy) but also keep an eye on the Open Source solutions (OpenOffice and DocBook) as anyone can submit a feature request and there is already plenty of interest in expanding the range of formats they can expand to.
Dedicated print software
Quark and Adobe's Framemaker are designed with this kind of job in hand but they come with a hefty price tag.
Word processing software
You possibly already have something that can do this for you in the shape of word processing software which can usually export in a variety of formats (including RTF, HTML and PDF). Examples include MS Word and OpenOffice's Writer.
XML
Possibly the most flexible solution - if you hold your data as XML you can apply XSL/XSLT to it and export it in a variety of formats. If your XML schema changes you only need to transform that. It would be advisable to use some kind of standard schema for this to reduce effort and make things as flexible as possible and there are initiatives aimed at exactly this - most importantly the DocBook schema.