I think best way to do this is via actions and filters, like we extend WordPress core itself.
Other options is like @helgatheviking pointed, if plugin is class you can extend it.
Unfortunately not all plugin developers provide useful filters and actions with their code, most often plugin isn’t written in OOP manner. Only way to save your modifications on plugin update, is to create copy of original plugin, change plugin name. I usually prefix original name e.g. Mamaduka Twitter Connect
, but with this solution you’ll need to manually update original plugin’s code.
If you think that plugin needs more filters/action, you can contact the author and ask him to include those hooks into the core.
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