The best replacement for mod organizer is nexus mod manager.

The best alternatives to mod organizer are rated as following:
★★★★★  nexus mod manager
★★★  wrye bash
★★  nmm

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Speaking about mod organizer, one probably shouldn't forget about boss.

Other search terms related to mod organizer and their ratings are:
★★★★★ boss
★★★ fnis
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mod organizer
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