My blog currently uses almost 20 plugins. For the most part I just tweak the CSS. However sometimes I modify the supplied php code to add/change some functionality. The risk here is that when the next upgrade comes along and I click the "upgrade automatically" function on my Manage Plugins page, I run the risk of overwriting my changes.
What would be great would be the ability to flag a plugin (on the Manage Plugins page) when you modify the base code.
Then when you click the "upgrade automatically" later on down the track (and you've forgotten that you modified it) it could warn you that you've flagged this as user-modified plugin so you can go upgrade however you want and maintain your changes (out of scope for this request).