This addon can automatically (semi-automatically) bridge several mesh islands in a smart way. It uses only boundary vertices and connect them with nearest boundaries of adjacent islands only. You can also set maximum distance for such detection. Something like “Fill holes”, but between mesh islands.
Screenshots for “Bridge islands” in action (just to demonstrate the idea)
Github: https://github.com/IPv6/kristallum/blob/master/blender/addons/sculptHelpers_v02.py
The inners are little hackish, but it do the work and may be helpful.
Addon also contain other operators, combined from different scripts found on internet.