How do I better organize my contacts on Galaxy Nexus? I remember when I was using my HTC Desire Bravo, it had this nice option to amalgamate duplicate contacts into a single profile contact. But in my Galaxy Nexus I am finding it cumbersome to do the same thing. Odd thing is these redundant contacts persist only on mobile - my Gmail doesn't have such data. I am thinking perhaps its the various other accounts I use along with Gmail such as Lync, Skype, Twitter, Facebook, etc.

my contacts spans around 4000.. I've tried Contacts+ and other apps but it didn't help. How Can I better organize the contacts and sync to my Gmail account?
From the stock People or Contacts app, find one of the contacts you want to merge. Click the pencil icon to edit that contact. Then from the overflow menu (click the three dots in the top-right), choose Join. Then click on the duplicate you want to merge this contact with. You can click Join again to merge further contacts with this one, or press the back button to go back to the list of contacts.

This works the same way regardless of where the contacts come from, and the merging is stored in the phone's contacts database, so it's available to third-party apps too.