I have over 200 links on yahoo site explorer, but only 2 on webmaster tools. Does anyone know why this is? My site is in the sandbox by the way, but i dont think that that effects the backlinks.
Google Webmaster Tools shows a sample of the links found for your site. To get more data, it sometimes helps to verify both the www and non-www versions of your site. Generally speaking, with 200 links you can probably also check manually to see if the pages linking are indexed in Google.
Also: not ranking for your site's name is not a sign that your site is in a "sandbox" (which technically doesn't exist anyway), but it does sound like your site might not be that trusted by Google's algorithms at the moment... which is something that I'd recommend working on more than just having the links show up in Webmaster Tools.
The two sites are indipendent and so Yahoo may have discovered links on pages that Google had not crawled yet. Another question to bear in mind is that Google group the link to the same site (if you click on that page you'll see the list of the website who links to you) while yahoo shows a row for each link.
Google doesn't show all of the links, at least not immediately, and they, sometimes but not always, tend to ignore certain types of links, such as nofollow links or links their algorithm considers suspect. Also, as Aurelio noted, they consolidate links sometimes. Yahoo shows just about everything their crawler finds.