I want to be able to track which sites are working for different campaigns.....some viral marketing and link baiting campaigns, other general SEO link building. If i used something like <a href="www.company123.com?site=1234">My Company keyword</a>, it'll work great for my link baiting tracking technique, but do search engines devalue the link because of the tracking code?
I have seen this have a negative effect in some cases. Well maybe that is a bit harsh but some engines will rank each tracking code. You might just try using something like Google Analytics and looking at the referral source instead. This way you have one link and can still see all the detailed stats.
is not it possible you to use 301 redirect from company123.com?site=1234 to company123.com? i think it will be the best seo for you tracking codes
They won't devalue the link, most php urls are like that. It does make it a little harder for the search engines to follow that type of url, not much though if it's that short.