If you're literally looking for variable storage, then
variable_get() are the way to go...during development. However - that means the variables are stored in the DB rather than the file system which can make deployment a bit painful later on. From your question, I assume this is what you are trying to avoid.
If you're looking to store sitewide configuration as opposed to just variables, then there are a couple of options.
I know you said you don't want Features, but Features 2.x is actually a MASSIVE improvement over 1.x, so if you've not ooked at it for a while I'd suggest giving it another go.
Disclaimer: I love Features 2.x :-)
Then there's Configuration Management which is an attempt at working some of the Drupal 8 CMI work to Drupal 7. It's relatively easy to use, and also pretty easy to extend.
On another note; Clive is kind of a Configuration Management evangelist - so if you have any difficulties with it then you have a wealth of information here.
Lastly, you could create a custom module that implements default configuration hooks (such as
hook_default_rules_configuration). A keen eye will notice that these hooks are a key element in getting configuration into Features :-)
Strongarm is also not dependent on Features, so you can utilise the Strongarm API yourself :)
I tend to use
$conf in combination with a Git-excluded
local.settings.php (see this question for a reason as to how and why) file for storing environment-specific configuration (such as site e-mail - things that might change between environment).