A few other groups now purport to be successors to the Popcorntime.io project, producing a "Popcorn Time community edition" (Popcorntime CE); of the different branches that popped up, none official.
What to avoid:
There's the "popcorn-time.is" branch [28], which is now located at "popcorntime.ag" [29]. This branch is made by yify.is (not the same as the original YIFY/YTS which shut down [30]); the dev team is still coding features and stuff for their branch, like loading movies off of google's servers rather through torrents. Unfortunately, the popcorntime.ag team engages in very sketchy practices. They have used fake accounts to promote their product [31], produced a fake subreddit (notice the extra "s") [32], impersonated popcorntime subreddit mods [33], lies about viruses in other projects to incite fear [34], etc. Their strategy for gaining users is to intimidate them by fear, and by impersonating legitimate sources. The are also other websites that the creators made, such as getpopcorntime.org [35], which are used to spam this branch. I would highly recommend users stay away from the ".is" and ".ag" versions. One of the developers of the original popcorntime.io explains his perspective on the issue as well [36], basically iterating a key point: users like projects that are not sketchy, where all of the app and code of the project is open.
The "safe" option:
There is also the "popcorntime.ml/tk" branch, which is now at the website "popcorntimece.ch" [37], which seems to have taken the community fixes, released them as a build, and stopped development. As of right now, it doesn't have any viruses, despite what the other branch may claim; at least, I personally didn't find any malware in the program. As of right now, it seems to be just basically a copy of the last version of popcorntime.io, with a few patches to replace YIFY and EZTV so that the program gets video torrents from different sources. More details can be found in the reddit post [38].
Ok, you skipped to the bottom, and don't care about the history as much... What should an average user do? (As of January 2016)
TL;DR If you're lazy, the current website for the Popcorn Time community edition is located at https://popcorntimece.ch/ for now. It's basically the last version of popcorntime.io with a few fixes to make it work, but don't expect new features.
I don't recommend using any other versions of Popcorn Time from other websites right now (including popcorn-time.se, popcorntime.ag, etc). They either contain malware, or engage in sketchy activity.
If you don't trust the popcorntimece.ch website, then just get the last version of popcorntime.io and patch it yourself. The directions to do this is in this reddit post: https://www.reddit.com/r/PopCornTime/comments/3sbsz6/download_working_installers_or_fix_your_current/
Alternatively, find a different product. Some users have reported success (and no malware) with Kodi or strem.io or other apps. I haven't used them myself, however.
References:
[1] http://www.pcmag.com/article2/0,2817,2454833,00.asp
[2] https://github.com/popcorn-time/popcorn-app
[3] https://web.archive.org/web/20140314235617/http://getpopcornti.me/
[4] https://medium.com/@getpopcornapp/goodbye-popcorn-time-93f890b8c9f4#.wiu7f88tt
[5] https://en.wikipedia.org/w/index.php?title=Popcorn_Time&type=revision&diff=681815665&oldid=681804053
[6] https://en.wikipedia.org/w/index.php?title=Popcorn_Time&type=revision&diff=666015740&oldid=666009818
[7] https://en.wikipedia.org/w/index.php?title=Talk:Popcorn_Time&oldid=687316485
[8] https://en.wikipedia.org/w/index.php?title=Popcorn_Time&type=revision&diff=643737636&oldid=643615969
[9] https://en.wikipedia.org/w/index.php?title=Popcorn_Time&type=revision&diff=637761615&oldid=637720113
[10] https://en.wikipedia.org/w/index.php?title=Popcorn_Time&type=revision&diff=632532279&oldid=632240283
[11] https://en.wikipedia.org/w/index.php?title=Popcorn_Time&type=revision&diff=631898075&oldid=631797507
[12] https://www.virustotal.com/fr/file/c6c56b2e2979e6bab471e7a77bd7e6ee23de06626838d7f5c2da43239fcabf9a/analysis/1396965513/
[13] https://en.wikipedia.org/w/index.php?title=Popcorn_Time&type=revision&diff=631738304&oldid=631733239
[14] https://github.com/popcorn-official
[15] https://git.popcorntime.io/
[16] http://popcorn-time.se/source.html
[17] http://popcorn-time.se/source/PopcornTime_Desktop-src.zip
[18] https://web.archive.org/web/20151024033921/http://popcorn-time.se/source.html
[19] http://web.archive.org/web/*/http://popcorn-time.se/source/PopcornTime_Desktop-src.zip
[20] http://i.imgur.com/hlxnmMh.png
[21] https://www.reddit.com/r/PopCornTime/comments/2lyxnm/time4popcorn_popcorntimese_now_includes_adware_do/
[22] https://vpn.ht/en/popcorntime
[23] https://torrentfreak.com/lawsuit-rumors-break-up-popcorn-time-team-151019/
[24] https://torrentfreak.com/popcorn-time-yts-global-outages-cause-concern-151021/
[25] https://torrentfreak.com/lawsuit-rumors-break-up-popcorn-time-team-151019/
[26] https://butterproject.github.io/
[27] https://github.com/butterproject/butter
[28] http://popcorn-time.is/
[29] http://popcorntime.ag/
[30] https://torrentfreak.com/yify-yts-shuts-down-the-end-of-a-piracy-icon-151030/
[31] https://www.reddit.com/r/PopCornTime/comments/3vagft/warning_about_yifyis/
[32] https://www.reddit.com/r/PopCornTimes
[33] https://www.reddit.com/r/PopCornTime/comments/3vagft/warning_about_yifyis/cxltb0w
[34] https://www.reddit.com/r/PopcornTimeCE/comments/40rrk5/warning_extremely_dangerous_trojan_virus_at/
[35] https://www.reddit.com/r/PopCornTime/comments/3vagft/warning_about_yifyis/cxlyinn?context=3
[36] https://getpopcorntime.org/
[37] https://popcorntimece.ch/
[38] https://www.reddit.com/r/PopCornTime/comments/3sbsz6/download_working_installers_or_fix_your_current/
