SQL Server 2008 upgrade advisor tool We upgraded to SQL Server 2008 from SQL Server 2000. But due to some legacy scripts/queries in our health care application, that run only in 2000, we had to run 2008 version on backwards compatibility mode. 

My question is what do I need to be aware of if I have to turn it on to full compatibility mode in terms of potential conflicts/issues etc. Is the Upgrade Advisor tool still useful in my case as we already upgraded but running in backwards compatibility mode. Is there value in running that tool? 

Any other information any one can share , will be useful.
The upgrade advisor will work, but you need to make sure to analyze a trace file of activity.  Just pointing it to the database and running it will only analyze the TSQL code stored in the database and not any TSQL code within your application.

In addition to the upgrade advisor, you can run a Profiler trace to capture the events: "Depreciation Final Support" and "Depreciation Announcement".  Both will identify code that will need to be evaluated because of syntax or reference to objects that don't exist in new version.

Check out Books Online for a decription of each of those events: Depreciation Event Category.