The Sony Reader apps on the Android market claim to be able to sync the reading position through your Reader Store account. I cannot test this claim because neither the apps nor the Reader Store are available in my country.
My solution has been to use root the Reader and install reader apps that do sync. I'm mostly using Kindle for Android (for Amazon content; has built-in sync) and the Aldiko reader (for all other content) in combination with Aldiko Sync, a small app that syncs Aldiko's content and reading positions using a Dropbox account.
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