This may have been somthing which was re-introduced in BizTalk 2006 or R2, but having a play with BizTalk 2009 I am glad to see the return of the double clickable functoid!
When I first moved from BizTalk 2000 to 2004, I was disappointed to see the loss of the ability to double click on a functoid in a map and be rewarded with the funtoid configuration window. I found that this was a backward step for BizTalk 2004 as far as developer productivity was concerned, as it added unnesessary steps which slowed the configuaryion process down - a major pain when maintaining or creating complex maps.
Having had a chance to begin using BizTalk 2009, this was one of the first things I noticed, and I'm pleased to see it back :)