Join lists by observing x-value

A couple of ways:

ds = Dataset1~Join~Dataset2
List @@@ Normal[GroupBy[ds, First -> Last]]
Last@Reap[Sow[#2, #1] & @@@ ds, _, List]

All yield:

{{20, {1}}, {30, {1.3, 1.2}}, {40, {0.4, 1}}, {50, {0.9, 
   0.4}}, {80, {1}}, {90, {1}}}

or

d1 = Rule @@@ Dataset1
d2 = Rule @@@ Dataset2
List @@@ Normal[Merge[{d1, d2}, Join]]

One way is to use GatherBy and then coerce the resulting list into the form you require:

d1 = {{20, 1}, {30, 1.3}, {40, 0.4}, {50, 0.9}};
d2 = {{30, 1.2}, {40, 1}, {50, 0.4}, {80, 1}, {90, 1}};

{#[[1, 1]], #[[All, 2]]} & /@ GatherBy[Join[d1, d2], First]

{{20, {1}}, {30, {1.3, 1.2}}, {40, {0.4, 1}}, {50, {0.9, 0.4}}, {80, {1}}, {90, {1}}}

A different way:

d = GatherBy[Dataset1~Join~Dataset2, First]
{Max[#1], #2} & @@@ Transpose /@ d

{{20, {1}}, {30, {1.3, 1.2}}, {40, {0.4, 1}}, {50, {0.9, 0.4}}, {80, {1}}, {90, {1}}}