Stack Overflow is running the same code as the rest* of the Stack Exchange sites.
There is, naturally, some degree of customization per-site.
On SO, you have:
- the interesting tab (and no active tab, though you can still get at it for now)
- meta.SO has [bugs] and [reqs] tabs, Stack Apps has the [apps] tab (I think that's it for custom tabs)
- code syntax highlighting for basically all the languages supported by prettify
- some SE sites have subsets of this (LaTeX on tex.se for instance)
- User searching is a starts with match, rather than a contains (due to # of users)
- Stack Overflow's meta is meta.SO, which is a fully fledged site
- all other network sites have a "proper" meta, with synced accounts
- ... except Stack Apps, which has no meta at all
- Some of the social sharing stuff is suppressed
- This is also true of all metas, SU, and SF
- Ads are served
- This is true of SU and SF too
Can't think of any other differences off the top of my head.
*stackexchange.com and Area 51 are different code bases though.