Now that you have it (hopefully) correct, let's speed it up.
First your latest modified code, unchanged, hopefully this is correct. I did remove the Evaluate[] when I realized earlier those were not necessary.
In[1]:= e[0]=1/2;
y[0,x_]:=Exp[-(x^2/4)];
w[x_]:=x^4/4;
e[n_]:=Integrate[y[0,x] (w[x] y[n-1,x]-Sum[e[j] y[n-j,x],{j,1,n-1}]),{x,-Infinity,Infinity}]/Integrate[y[0,x]^2,{x,-Infinity,Infinity}];
y[n_,x_]:=y[0,x] Integrate[(1/y[0,t]^2)*Integrate[y[0,s] (w y[n-1,s]-Sum[e[j] y[n-j,s],{j,1,n}]),{s,-Infinity,t}],{t,0,x}];
In[6]:= Timing[{y[5,x],e[5]}]
Out[6]= {450.457*Second, {((-916731*x^2)/512 - (651363*x^4)/2048 - (89673*x^6)/2048 - (69107*x^8)/16384 - (250183*x^10)/786432 - (29177*x^12)/1572864 - (1325*x^14)/1572864 - (269*x^16)/9437184 - (25*x^18)/37748736 - x^20/125829120)/E^(x^2/4), 916731/256}}
Now kill the kernel and restart with a tiny change to your code
In[1]:= e[0]=1/2;
y[0,x_]:=Exp[-(x^2/4)];
w[x_]:=x^4/4;
e[n_]:=e[n]=Integrate[y[0,x] (w[x] y[n-1,x]-Sum[e[j] y[n-j,x],{j,1,n-1}]),{x,-Infinity,Infinity}]/Integrate[y[0,x]^2,{x,-Infinity,Infinity}];
y[n_,x_]:=y[n,x]=y[0,x] Integrate[(1/y[0,t]^2)*Integrate[y[0,s] (w y[n-1,s]-Sum[e[j] y[n-j,s],{j,1,n}]),{s,-Infinity,t}],{t,0,x}];
In[6]:= Timing[{y[5,x],e[5]}]
Out[6]= {12.628*Second, {((-916731*x^2)/512 - (651363*x^4)/2048 - (89673*x^6)/2048 - (69107*x^8)/16384 - (250183*x^10)/786432 - (29177*x^12)/1572864 - (1325*x^14)/1572864 - (269*x^16)/9437184 - (25*x^18)/37748736 - x^20/125829120)/E^(x^2/4), 916731/256}}
That is a very tiny change that makes this 35 times faster, and will make it far far far far faster if you are going to try n=200, that should not break the mathematics. It is just a Mathematica trick. I'm not even going to try to explain it.
As always, check this, test this, verify this is correct. It is way too easy to type a bunch of stuff in, get something out that isn't obviously completely wrong and think you are done.
Note: If you are going to use Mathematica, particularly if you are going to attack big problems then you should seriously consider getting the fastest CPU and memory that you can afford. A good recent fairly fast I5 or I7 or a comparable AMD CPU along with 16 or 32 gig of memory, all dedicated to the sole task of running Mathematica, will make your life much easier. But, even with that, some problems are hard and take a long time, even if you have written the best code implementing the best algorithm that you can, and it is not uncommon to wait hours or even in extreme cases weeks or months to get a solution for a really hard problem.