100000 of rows is not really large ammount for MySQL. I have no idea how Perlmonks does it but basic schema should be trivial. Something like:

create table vote (
    /* primary key */
    vote_id unsigned not null auto_increment,
    primary key (vote_id),
    /* reference on record in table which stores users */
    user_id unsigned not null,
    /* reference on record in table which stores nodes */
    node_id unsigned not null,
    /* vote value: adjust field type for your requirements */
    value int not null,
)
[download]

It is very likely that also indexes for person_id and node_id fields are needed. It is very likely to have those fields in WHERE part of queries.

--
Ilya Martynov (http://martynov.org/)