First off, here are two very useful threads/posts on the subject:
http://boards.na.leagueoflegends.com/en/f/cIfEodbz/d/5kx4F7VE
http://boards.na.leagueoflegends.com/en/c/player-behavior-moderation/5dmkJinG-3rd-party-applicationsmodifications-whats-allowed-and-what-isnt
Secondly, the condensed version of Riot's stance regarding custom skins:
For now, custom models and artwork sit firmly in a "use-at-your-own-risk" category, but we're keeping an eye on them. We can't optimize for assets we don't develop, and if they do become a concern in the future (ie. they provide measurable player advantage), we'll take action based on the stance we just discussed.
All that said: Some programs have other features that are not allowed as per Riot's policy. If a program has those features, regardless of whether you use them, that program is not allowed and can get you banned. So either way I recommend you read the OP's of the aforementioned thread to be safe and get an idea what Riot is looking out for.
I'd love to also tell you what programs are safe to use, but unfortunately I don't remember the names right now and I certainly don't want to give you a wrong one.