I have been going through the painful process of merging and cleaning up my contacts from Gmail, two Google Apps accounts, Outlook, and a few other sources. I have managed to get them all into Gmail but it has been a real pain to keep them in sync and merged and disseminated to my BlackBerry and PlayBook. Jason told me to check out Scrubly as a solution for removing duplicate contacts and merging contacts along with backing it up into a central location.
I am currently trying out their free plan for up to 250 contacts which seems to work nicely. They have two plans for those serious about cleaning up their contacts. For $19.99 you can do a one time clean up for an unlimited number of contacts. For $39.95/year you get unlimited contacts and unlimited scrubs per year.
Check it out at www.scrubly.com