First it was beetles. You can get 300-400k easy in only 30 minutes. I stopped because I got bored of doing it so often.
Then I switched to turnips. You can make millions a week with minimal effort. I stopped because after Pokemon X/Y came out, there was less people with high turnip prices around to visit.
My main income since then has mainly been selling stuff on the ReTail board here on TBT. Depending on the items sold, this hit and miss on whether it's more efficient than beetle hunting. However, since I'm at the point where I have most of the items available in the game, I don't have much need for bells. So I don't even do this very much anymore.
My main source of income is just digging up/selling fossils and searching for the money and gem rocks each day. I only get a chance to play for 15-20 minutes a day, but all that usually nets me around 30-40,000 Bells each day.
Other than that, I occasionally go to the island to do some beetle hunting, but that seems to be a rare occurence for me as of late.
Prior to resetting my town, it was turnips. Since the reset, it's beetles because it's a more reliable source. Once my mayor's house is fully expanded again, I'll go back to turnips.
I grow loads of perfect fruit trees at once and keep harvesting them until my storage is completely full, then I sell them at other towns! I get about 5 million bells each time.