Best way of storing 'website settings' data in a database table?

A row for each distinct option setting, using name/value pairs one per row, is probably the best way to go. It's more flexible than lots of columns; if you add an option setting you won't have to run any kind of ALTER TABLE operation.

The WordPress wp_options table works this way. See here. http://codex.wordpress.org/Options_API

If you had a "compound" option, you could serialize a php array to store it in a single row of the table.

First of all i would considere one more thing, a configuration file...

Then you should ask yourself what you need for your project...

First of all i would considere config file vs database :

The big advantage of databases options over a config file is the scalability, if you have many applications / sites requiering those configurations then go for the database as it would avoid you to copy several times the same config file with all the problem of versioning and modification of the file on all those different "sites"

Otherwise i would stick to the config file as access is faster for an application and the file may still be aviable in case of sql server outage in which case some config may still be relevent, the config file may also be include by your versioning software. For some security reason as well, imagine your DB is shared among many softwares ...

Then if you stick to database i would recomand the one row one label one config, i considere it easyer to manage records than table structure, specially over time and over evolution of your software.If other dev join your project your table structure may quickly become a big mess :]

The final arg is security... a good practice is to set the "DB user" form a software to a user which dosen't have DB structure modification rights, only the right to access/moidify delete records ;)

The two ways works fine. I would say that if you want to administrate those settings in an admin panel, the one setting by column is better, because you can add new settings on the fly with a simple INSERT query from your admin. Which is better (more secure) than an ALTER TABLE query.