virus on my home pages

[#1]

I was emailed by a visitor to one of my web sites who said that I had JS/ downloader infection on my home pages.  I found that there was code on the page (just after the body tag) that I had not put there.  I copied this code in 2 parts to notepad files and uploaded the correct index page again.  I then checked my other sites and found that 4 out of 6 all had the same code on them. 
I am obviously concerned as to how this could have happened and about it happening again.  Any advice would be appreciated
Thanks

[#2]

Whats you site so we can look at it. Normally the js code is from some util you have added to your site like a webcounter or some sort of display. This calls a routine on the providers server and normally does its intended job but if its changed the other end it can do anything.
Its not that often it happens but Google has had it happen to some of its code this week.
Remove any js code which you dont know what it does but if you are using buttons they sometimes use js as well

[#3]

One of my sites is www.soothemassage.co.uk. ; I have taken the suspicious code out of it now though.  The code is mainly number and letters not like html, php or javascript
Thanks

[#4]

the line on your first page is wrong
file:///H|/WEBS/soothe_therapies_at_ramada.htm"
and all the lines for the links at the bottom as they are pointing to files and dont work. It seems the same on every page that all the links at the bottom dont work.
I would be worried about putting your certificates on the web as I can now save them, clone them and take over your ID.
I get no virus warning from the pages so you seem clear

[#5]

Thanks,
for the advice, I'll get those changed.
What I am really concerned about is how that code could have got onto my web pages, any ideas.  Or what I need to do to stop it happening again

[#6]

As I said its something you put there it often comes via visitor counters or similar.
You innocently put link like www.nice.co.uk/stop.php this puts up a ling or web page states.
Now if someone changes the file stop.php on the other server it could be used to do anything like send visitors a virus.
It wont be anything you have done directly as if you are running AV at home and preview the site it should pick anything up.
Worth just doing a virus scan on your pc.
As i said even Google had its advert high jacked with a virus last week so it can happen to anyone. You didnt have any Google adds on did you?

[#7]

Quote from: samuria

As I said its something you put there it often comes via visitor counters or similar. You innocently put link like www.nice.co.uk/stop.php this puts up a ling or web page states.

I never added that link and when I searched my local site I could find no mention of it.  I have re-uploaded my entire local site.  THough yesterday I had changed those incorect links in a template so I uploaded all the pages that were based on it and they should have been all the pages on the site

Quote from: samuria

Now if someone changes the file stop.php on the other server it could be used to do anything like send visitors a virus. It wont be anything you have done directly as if you are running AV at home and preview the site it should pick anything up. Worth just doing a virus scan on your pc. As i said even Google had its advert high jacked with a virus last week so it can happen to anyone. You didnt have any Google adds on did you?

No I haven't ever had any google adds.  I run AVG and it hasn't found any viruses on my home pc.