I believe many SQL Server DBA's can leaver off the Oracle OFA (flexible architecture) in terms of structuring data/log and install directories for your SQL Server databases. Generally its all common sense though.
I tend to following this:
this will change slightly if we are also using Oracle or another DB on the same box.
The standards flow into the location of your binaries and importantly, your backup files!
In terms of large numbers of DBs on a box and bucket loads of database files, its very difficult to come up with some magical solution, especially when most have very different IO characteristics. The generic RAID-5 solition is a generally a good one for probably 80% of cases (especially in hosted envs). The trick here is a large cache and leaving write/read on at the controller.
Author of "SQL Server Backup, Recovery & Troubleshooting"
Author of "SQL Server 2k for the Oracle DBA"