SQL Server 2000
1.Security:Owner = Schema, hard to remove old users at times
2.Encryption:No options built in, expensive third party options with proprietary skills required to implement properly.
3.High Availability:Clustering or Log Shipping require Enterprise Edition. Expensive hardware
4.Scalability:Limited to 2GB, 4CPUs in Standard Edition. Limited 64-bit support.
SQL Server 2005
1.Security:Schema is separate. Better granularity in easily controlling security. Logins can be authenticated by certificates.
2.Encryption:Encryption and key management build in.
3.High Availability:Clustering, Database Mirroring or Log Shipping available in Standard Edition. Database Mirroring can use cheap hardware.
4.Scalability:4 CPU, no RAM limit in Standard Edition. More 64-bit options offer chances for consolidation.