What is the best test for statistical analysis of treatment groups at baseline and different time points?

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Igor Eloi

By "missing values" do you mean NA or different sample sizes?

Maybe you will be better off using Kruskal-Wallis test. It is very flexible and you could easily found adaptations to suit your data.

Seyed Mahdi Amir Jahanshahi

As you mentioned, the the general methods are repeated measurements and one- way ANOVA which are belong to parametric techniques and Friedman test which is belong to non-parametric techniques.

I suggest you to replace your missing values then use one of the mentioned methods?

Rainer Duesing

A robust method to handle repeated measures and missing data is multilevel modeling aka hierachical linear models aka linear mixed effects models.