Okay, it seems here is nobody with some experience and know-how about this topic.
Anyway, here is my current work in progress list of research:

sadly no API provided:

• google.com - the web front-end is just great

• xMarks

• morebookmarks.com - asked via email for API support - answer: "Morebookmarks has no api. Good luck in your search."

• vizited.com - a lot to many features, but where is the API ? - UPDATE: Got a reply, no API: "Currently we do not have any kind of API. We're still developing Vizited and adding new features and we will put your request on our list."

asked visa support page or email for third party API - no reply yet

• skloog.com - first impression was good

• favilous.com - very slow site

• deskhot.com - small private project, does EXACTLY what I'm searching for perhaps except the remarks, those are missing - but sadly I'm afraid the owner wouldn't provide a API

perhaps / undecided / where is the API?

• connotea.org - first impression is okay but a very strong social aspect - this is clearly not the scope of my project

• instapaper.com - good, but not really a pure bookmark organizing, more a storage service

• blinklist.com Tested it with several browsers and at the Internet Explorer I had some very serious bugs, after reloading the page I was suddenly logged in as a different user and was able to see and edit his list - I'm scared

no option for my project:

• pinboard.in - membership fee needed - $9.52

• zootool.com - If I wan't to sign up there is a message that this site currently only supports Safari, Google Chrome and Firefox - not platform independent enought!

• diigo.com - I'm not really able to find a webpage on this site where I'm able to manage my Bookmarks like at google.com - I need some kind of extentions or bookmark scripts to manage it, I don't like it

• historio.us - confusing, not really a bookmark service for me

I'm currently very frustrated. I don't know why some big company like google doesn't provide something useful like this.

UPDATE: Got a answer from vizited