This one is actually a tricky question. So far, Riot has not banned the use of custom skins, but they are allowed in a "use at your own risk" capacity. Which means, if at any time part of the software that you use is found to have aspects of it that give an unfair advantage, they will be blacklisted. While you might think you are just running the program to load in a cosmetic skin, many of the custom skin programs actually have other aspects to them that are NOT allowed. And Riot has stated that using the program for skins only, even if you claim not to use the other parts, is still a punishable offense. Oh, and one last thing... I would be very cautious with regards to using sites/softwares that are claiming to give you free "versions" of existing Riot skins. Just my personal opinion on the matter, but I wouldn't do that under any circumstance; legal reasons, copyright, etc.
I highly recommend this thread by Wuks, because he's very thorough, and if you read through the comments, people have mentioned some of the different programs that have been approved/banned over time since the thread was created:
http://boards.na.leagueoflegends.com/en/c/player-behavior-moderation/5dmkJinG-3rd-party-applicationsmodifications-whats-allowed-and-what-isnt
tl;dr Just be cautious with the custom skin software you use.