I noticed the same things that others have mentioned: file growths and sizes, tempdb, filegroups...
I have always been advised to use a set size, rather than percentage, for file growth. I have participated in a Microsoft SQL Server RAP, and they advised us to do things in increments of 1024MB.
So I set all all my file growths and sizes in multiples of 1024M.
I realize you wanted us to focus on settings we can see from the monitoring tool, but I am curious about instant file initialization, ad-hoc optimization, asynchronous update stats, etc.
Is there a way to customize what the tool shows you?
Regarding TempDB and the number of files, I was not able to find how many cores are on the servers.
What about separating TempDB MDF and LDF?
Also regarding separate filegroups for non-clustered indexes. In addition to the possible IO related benefits, I find that there are several administrative benefits, as well. For example, you then have more flexibility in where you locate your files, you can take filegroup backups, you can do filegroup dbcc checkdb commands, etc.
The forums database seems to be using full text filegroups. What about locating them on a separate file system from the regular data files?