I never looked around too much, but I found a great one on the island above the rustburo city area.
EDIT: Route 115, the northern part, the tree.
EDIT: RETURN OF THE EDIT:
http://wiki.answers.com/Q/What_is_the_best_secret_base_spot_on_pokemon_emerald
And according to wikianswers, this is the biggest.
I can't post URLs yet, so meh.
YESH
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I don't us hacks, I don't cheat, and I don't EV train.