What is the best way to name smart lists?

I'd start them with a two digit number that skips a number or two so you can easily organize them and add in a custom step if needed. 

I love putting things in folders to organize them, but it depends on what kinds of smart lists you're talking about...are you talking about the My Smart Lists folder in the Lead Database?

For My Smart Lists, you want to do this:

Standard Folders for global lists
People folders for each user

Naming: see this document
http://www.slideshare.net/jdavidhill/naming-and-organizing-your-marketo-instance

generally I use something descriptive:

Product Name - Customers - EMEA

I keep a lot of my smart lists associated with the programs. Then, when pulling a larger list, you can use the ones you have already created.

Naming for the lead database is up to you, but if you use folders and sort by area/type of list you're pulling, that tends to be most helpful. Also, don't forget about segmentations! Those always help when pulling smart lists.