Positioning of the CLR in SQL Server 2005
Microsoft have published a White Paper on the positioning of the CLR in SQL Server 2005. It could have been called a "Best Practices Paper"
http://msdn.microsoft.com/data/default.aspx?pull=/library/en-us/dnsql90/html/sqlclrguidance.asp
Using the CLR as a full T-SQL replacement would be a big mistake as it is not as efficient in all areas as T-SQL is. Their usage scenarios are credible and as far as I have used the CLR functionality, is about as far as I would go, before hurting performance.
If the CLR was a full T-SQL replacement, SQL Server would be called CLR Server. Just remember that when designing your applications.