Email validation aside...Email validation aside...

Switching between GUI input and console output

You take your input via a JOptionPane, but the output of your validation is displayed via System.out. It will be much better UX-wise to show the result as another dialog box too.

Braces

Please use braces, it's not that hard. One extra line here or there and your conditions/loops will look even messier to clean up.

Boolean assignment and evaluation

if(dot1==0)
    dot=false;
else dot=true;

This can be rewritten as dot = dot1 != 0.

while(at==false||domain==false||dot==false||tld==false)

This can be rewritten as while (!(at && domain && dot && tld)).

And speaking about variable names...

Variable names

It's not easy to decipher what do at1, at2, dot1 etc. mean. It's recommended to use more descriptive names here, e.g. hasTLD.