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I never got into troubles, since I don't use it for spamming purposes. It is a lot less maintenance than cloaking for all those clients who cannot afford it. I never uses this without my clients written consentement.
I use doc type declarations on all optimised pages so redirects occurs for valid reasons.
I noticed everything is fine by hiding those scripts in a protected folder.
I suggest you will benefit staying miles away from meta refresh.
I will try to make sense explaining this, OK? (read it with a French accent à la Cluzo for more fun) :)
I am really not sure about how this can influence SE positions or avoid beeing penalised for using JavaScript redirects. I will not pretend it helps in any way, but serving valid HTML products seems to be a good idea in general, so I just do that to keep on the safe side.
Part of pages optimisation is to make them W3C valid HTML. Any valid HTML pages start with a "dtd" or document type declaration. This segment is supposed to tell the browser wich kind and version of HTML document it deals with so it can render them faster. I don't know if any spider read them.
I use redirects mainly for framed sites. Generally, I promote existing sites I do not build them. So I choose the closest dtd that fit. This is to avoid that some main page beeing found on some search engine and beeing displayed without navigation or eye candy frames. I make sure that all redirects lead to a proper frameset.
For instance main pages will use this dtd:
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
"http://www.w3.org/TR/html4/loose.dtd">
The redirect will call the frameset this page is supposed to be opened in that will have this dtd:
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Frameset//EN"
"http://www.w3.org/TR/html4/frameset.dtd">
I have a couple of "guinea pigs" sites wich I own and that I use for experiments. I have not tested yet for any difference in page rank with HTML validity alone.