The Channel Queries service queries channels for information about them (in terms of topic and modes) as well as their lists of participants. It does this shortly after having joined a channel, as a service to all other plugins, so they don't each have to independently do it themselves.
The Connect service handles logging onto IRC servers after having connected, as well as managing authentication to services. It also manages responding to PING requests, and capability negotiations.
The CTCP service handles responding to CTCP (client-to-client protocol) requests behind the scenes.
The Persistence service keeps track of all encountered users, gathering as much information about them as possible, then injects them into IRCEvents when information about them is incomplete.
"Service"-level plugins, used to carry out tasks behind the scenes.
Removing or disabling any of these may yield adverse results.