I use SublimeText 2’s portable version. Whenever a new build is released and I download it, I basically extract it right over the old folder. As long as I keep all my own snippets in the data/Packages/User directory, they don’t get overwritten. But I’m pretty sure other files get overwritten, like default preferences, etc… I realize that certain preferences I should move to user-specific preferences.

Anyways, my question, is there a specific procedure to upgrading the portable version of Sublime where you keep all your existing settings, snippets, etc? Do all custom snippets and packages need to be stored in the User directory and all program-related settings need to be stored in user-specific profiles (which I assume are stored in the User directory also)? What about macros? Build scripts? Etc?

Basically I just want to upgrade versions without loosing settings and custom features…

I do the same thing—copy the new portable version over the old.
If you upgrade the non-portable (installer version) it will over-write your default prefs in the same way that copying the new portable version will. Because of this, any user prefs should be in the User directory (e.g. user file settings instead of default file settings).
However, you are free to put other folders in the Packages directory—Sublime won’t delete them or anything. The only thing you need to put in the user directory is extra copies of any files that Sublime is packaged with that you’re editing.
Let me know if that’s clear.