I prefer A to B, B to C linking structures (a method of non-direct linking). However, solid link exchanges (A to B, B to A), work just as well-- As much as people still like to discount it.
As for the PHP thing, Googlebot will follow most PHP URL Strings, but not strings like
http://www.sitename.com/jump.cgi?=2435
I'd avoid any type of PHP linking to your link partners, as Google does not pass on PR through such linking methods (and apparently, link exchanges have gone so far as to depending entire upon PR).