There are some apps in the marketplace that can help you by listing and sorting custom fields by name or type, but that's only helping, not actually doing the work of finding duplicates.
Identifying duplicate fields is a manual task, a human, one with understanding of the reasons people may be adding fields or the knowledge of who to ask, needs to go through the list and analyse it looking for each possible duplicate. Jira, and in fact, most software, has no way of knowing that a text field called "Mr Flibble's Cousin" might be a duplicate of a select list called "Type of Penguin"
Once you identify a duplicate, then deleting it is straightforward, BUT, you will be destroying all the data in it on all the issues. So you may want to look into merging the content into the field that is being duplicated, and you'll need to think about how it might clash.
In the example above, if "Mr Flibble's Cousin" is "Emporer", and "Type of Penguin" on issue BIRD-42 contains "Multi-molared Rockboldt", then you need to decide whether to drop Emporer, or add Emporer to the options list and set it on BIRD-42, losing the "multi-molared Rockboldt" that already exists.
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