I can set upload limit for web application in SharePoint 2010. But cannot do it for specific site collection?
OOTB there is no way to control this property at site collection level. You can set it at Web Application level but not for site collection.
as a workaround, you need to write some kind of custom code to do it at site collection level. check this
another workaround is, if there are multiple site collections which need higher upload limit, you can think about creating a new webapp and move all site collection their. but this has some pros and cons.