You should be able to call most commands from a private message with the bot. Using help <plugin> <command> will explain each command.
Admin: acmd, capability add, capability remove, channels, clearq, ignore add, ignore list, ignore remove, join, and nick
Alias: add, beer, beer2, beerme, changeset, codereview, cokeme, cr, cs, dcme, define, facts, google, googledefine, hi, holidays, jira, list, lock, mailinglist, powerup, psu, refer, remove, requestsvnspace, review, scrumoff, scrumon, test, test2, ticket, and unlock
Channel: alert, ban add, ban hostmask, ban list, ban remove, capability add, capability list, capability remove, capability set, capability setdefault, capability unset, cycle, dehalfop, deop, devoice, disable, enable, halfop, iban, ignore add, ignore list, ignore remove, invite, kban, key, kick, limit, listbans, lobotomy add, lobotomy list, lobotomy remove, mode, moderate, nicks, op, part, unban, unmoderate, (1 more message)
ChannelStats: channelstats, rank, and stats
Config: channel, config, default, export, help, list, reload, search, and setdefault
Factoids: alias, change, forget, info, learn, lock, random, rank, search, unlock, and whatis
Herald: add, change, default, get, and remove
Karma: clear, dump, karma, load, and most
MeetBot: addchair, deletemeeting, listmeetings, pingall, recent, and savemeetings
Misc: apropos, clearmores, completenick, help, last, list, more, noticetell, ping, source, tell, and version
Owner: announce, defaultcapability, defaultplugin, disable, enable, flush, ircquote, load, logmark, quit, reload, reloadlocale, rename, unload, unrename, and upkeep
RSS: add, announce add, announce list, announce remove, ci, info, remove, rss, and talk
Reply: action, notice, private, replies, and reply
Seen: any, last, seen, since, and user
Services: ghost, identify, invite, nicks, op, password, unban, and voice
ShrinkUrl: expand, tiny, ur1, and x0
Status: cmd, commands, cpu, net, network, processes, server, status, threads, and uptime
User: capabilities, changename, hostmask, hostmask add, hostmask list, hostmask remove, identify, list, register, set password, set secure, stats, unidentify, unregister, username, and whoami
Web: doctype, fetch, headers, size, title, urlquote, and urlunquote