While manually maintaining separate copies, it's easy to have created duplicate and/or slightly different copies of what were meant to be the same entries. There are also scenarios where a corrupted OS X's Sync Services can result in duplicate iCal entries which can then get sync'd to other information sources.

There are 3 strategies for removing duplicates:

1. manually delete the duplicate entries in one information source and those deletions will then be sync'd (subject to your setup options) with the other information source(s) during the next sync
    
2. if applicable, use one of the resources mentioned at
   http://www.nhoj.co.uk/icaldupedeleter/ or
   http://www.hawkwings.net/2006/05/16/ical-de-dupe-kill-ical-duplicates/
    
3. for advanced users: if all the information exists without duplicates in one of the information sources, you can do the following:
• if you're not familiar with the Advanced Setup, you'll need to download and watch the tutorial video
• check/enable the "Show Advanced Sync Setup" option via the "Preferences" tab in the Sync'Em preferences
• to be able to recover from any problem, make a backup of each source that contains all the entries and, for extra "insurance," of all the other information sources
• via the Advanced Setup, for each of the other Sync Sources (i.e., the ones with duplicate entries):
• in that information source, delete all the entries
• make note of that source's "Sync Source" and "Access Sync Source Prefs" settings
• delete then re-create both that source's "Sync Source" and "Access Sync Source Prefs" settings
• at the next sync, those reconfigured sources will be sync'd as initial/full syncs (subject to your setup options) with the contents of the other/full/non-duplicate source(s)

You may also want to see the FAQ about duplicate contact entries.