Weka only has its ReplaceMissingValues filter for dealing with missing values, which just uses means and modes as replacement. However, this approach is not always the best. Hence I started on a Weka package project some time ago to offer other techniques as well (also available through a preprocessing filter). However, that kind of stalled a bit. A colleague of mine, Lyn Hunt, had a student testing various techniques a while ago and I will use this opportunity to breath some new life in my project by integrating these techniques. 🙂
You can find the project here:
https://github.com/fracpete/missing-values-imputation-weka-package