Perhaps this is more proper way to set this up, but it potentially could be simplified further. Please note the different way to set up the Manipulate control.

Man29okt16={{0,1},{2.30,2},{3.55,4},{6.23,4},{6.35,3}};
Man30okt16={{0,4},{2.39,4},{5.55,4},{7.15,4},{8.28,4},{9.14,4}};
Man31okt16={{0,2},{2.38,3},{5.10,3},{6.08,4},{7.02,4},{7.52,3}};
Man01nov16={{0,3},{3.27,4},{5.12,3},{5.38,4},{7.23,3}};
Man02nov16={{0.0,3},{3.36,3},{5.05,3},{6.18,3},{8.05,3},{9.30,3},{9.55,3}};
Man03nov16={{0.0,1},{3.54,2},{7.13,3}};

Manipulate[
    ListPlot[{
       Man29okt16,Man30okt16,Man31okt16,
       Man01nov16,Man02nov16,Man03nov16},
    Joined->True,PlotLabel->Style["Title",Bold,20],
    BaseStyle->{FontFamily->"Helvetica",FontSize->9},
    LabelStyle->Directive[White,FontFamily->"Helvetica",15,Bold],
    PlotLegends->LineLegend[{"29okt16","30okt16","31okt16","01nov16","01nov16","02nov16"},
    LegendLayout->(Grid[#,Spacings->{1,.6}]&),LegendLayout->"Row",
    LabelStyle->Directive[Black,10]],GridLines->{{1,2,3,4,5,6,7,8,9,10,11,12},Automatic},
    GridLinesStyle->Directive[White,Dotted],
    FrameTicks->{
       {Automatic,Automatic},
       {{{0,"0:00"},{1,"1:00"},{2,"2:00"},{3,"3:00"},{4,"4:00"},{5,"5:00"},
       {6,"6:00"},{7,"7:00"},{8,"8:00"},{9,"9:00"},{10,"10:00"}},Automatic}},
    FrameStyle->White,PlotRange->{{0,11},{0,4.3}},Background->Black,ImageMargins->1,
    FrameLabel->{"Time","Y-axis"},Frame->True,InterpolationOrder->0,ImageSize->500,
    PlotStyle->{
       If[MemberQ[stats,29],Thickness[0.01],None],
       If[MemberQ[stats,30],Thickness[0.01],None],
       If[MemberQ[stats,31],Thickness[0.01],None],
       If[MemberQ[stats,01],Thickness[0.01],None],
       If[MemberQ[stats,02],Thickness[0.01],None],
       If[MemberQ[stats,03],Thickness[0.01],None]}],
{{stats,{29,31},"check"},{29,30,31,01,02,03},CheckboxBar}]