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Well, anything you purchased from iBooks is currently stuck. That DRM is not as yet able to be circumvented. The only think you are going to be able to do with those is store them in Calibre and continue to read them on Apple Devices.
As for your old Sony books. Personally I'd try to get anything in LRF format converted or redownloaded into ePub or Mobi. If they are DRM'd, you will need to remove the DRM and then convert the file format. There are numerous threads populated around MobileRead on where to go to find the tools to accomplish this.
Generally there really is no problem with storing multiple copies of a book in Calibre in different formats. For the most part eBook files are tiny and Calibre will do a very good job of choosing the best format for the device you are sending it to.
I would strongly suggest you remove DRM wherever possible though - otherwise you could very well be in the situation 10 years from now where you want to reread a book and you can't remember what account or Device you bought it for. It is a real pain in the butt.
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