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Personally, I'd advise rewriting them if possible. Nice, short, clean URLs are a plus both for search engines AND users who may e-mail them, or even key them in. And, by all means, don't use session IDs - they are a killer for getting properly spidered and indexed.
Regarding clean linkage:
I have a footer link from a big directory site with over 30 pages with PR4 and up (top is PR6)
The link is (#1) www.xyz.com/index.php?id=5&b=5 Anchor text is about 40 chars.
I have a strong feeling that 2 index.php file parameters scare away GoogleBot from counting this as a backlink.
Another idea is that GoogleBot sees a long anchor text (+ suspects some sort of trap from index.php parameters) and this is whay axes these links.
Yet another idea is that PR of the page is not high enough for google to consider this link eatable.
Yet another idea it's the combination of the four mentioned above.
I personally saw links of the sort:
(#2) www.somebodyssite.com/rt.phtml?uid=1231&url=http://www.xyzzz.com
or
(#3) www.somebodyssite.com/cgi-bin/go.cgi?http://www.xyzzz.com
registered as a backlink for www.xyzzz.com and visible when doing link:www.xyzzz.com search.
Programmingwise those three links look the same to me (especially #1 and #2).
Any other variables to consider?
Anything that I'm missing here?