In the series finale we discover who he is and what he does. Josie's Clone explains to Josie that The Janitor is "An Observer of Observers" who comes from "further along the time line than anyone can imagine". Essentially, The Janitor is part of a group from incredibly far into the future which is charged with making sure the time line is kept intact and advises other Observers who come from earlier points in his time line.
Presumably the Janitor is far more evolved than standard humans. This is shown by appearing the same age in different, and distant, points in time (although it is unclear if he time traveled to these points or if he lived through them).
In the series finale, the Janitor is stranded in the present (2006) without the possibility to return. He is presumably living a normal life and possibly a janitor in the new Blake Holsey High.