The php files are about the only thing you have to worry about changing and with the plugin system not many hacks require file edits these days. If you upload new php files you will have to make the same changes you made in any mods.
Templates may be updated in newer version of vb, but with 3.5 it will tell you which ones have changed and you can view your old and new and see what is different.
Most plugins should carry over. There would only be issues if they change the way things work in the core vb and the plugin needs to be updated to use the new methods.
A good merging tool can help with both of these updates. I would suggest araxis merge, but most people like winmerge.
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