Best Practice for Folder strucure? I don't like my data files in C:\Program Files... , especially with a new system that has a smallish SSD as C: which holds mainly the operating system.

So on a recent install I put my data files into D:\apps\MSSQL\DATA

Where do you put your Sql Server data files, if you are not going with the default?

I am mainly looking for good habits to make my sql server deployments easier to use.
Never on C:\ if it can be avoided, though with smallish SSDs and VMs on laptops it's hard to have anything but C:.

So where else? Depends on the config. I've done like you for simple workstation installs: data, logs, tempdb all on D:. But then you get into more advanced implementations where you have a SAN and many spindles to choose from - there I've had groups of data files on M:\ and N:\, log files on L:\, tempdb on T:\, etc. Making deployment easier isn't the only goal you should consider... it's also reducing the need for re-deployment and/or moving of data/log files later. :-)