The best replacement for nexus mod manager is steam workshop.

The best alternatives to nexus mod manager are rated as following:

★★★★★	steam workshop
★★★★★	fomm
★★★★	mod organizer
★★★	fallout mod manager
★★	wrye bash
★	oblivion mod manager
	skyrim mod organizer

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Speaking about nexus mod manager, one probably shouldn't forget about fose.

Other search terms related to nexus mod manager and their ratings are:

★★★★★	fose
★★★	skyrim script extender
★★	skse

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Google Trends

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nexus mod manager

steam workshop

fomm