We are about to undertake a rather large customization of SharePoint and I wanted to get some feedback prior to jumping in with both feet. One of the issues we are kicking t
We deploy it to the 12 hive as part of our free SharePoint Infuser tool, which you may want to consider to deploy JavaScript (inc JQuery) to multiple pages in one go without using any messy changes to masterpages, core.js etc.
Internally it uses the delegate control approach proposed by Ric above, it is just a more generic solution and can be used for all kind of purposes.
For details see http://www.muhimbi.com/blog/2009/07/massage-sharepoint-into-submission.html. For a very powerful example of what this makes possible, see http://www.muhimbi.com/blog/2009/07/automatically-add-search-as-you-type-to.html