All of them are the same, all of them have the same Pokemon in them, Aipom, Cherubi, Burmy, Munchlax, Heracross, Combee and Wurmple. There is no such "good honey tree". The one in Flotoma Meadow is propabaly the best one because you can get honey easily from the man there.
There's no good or bad honey tree but munchlax only appears on four random trees for every game if I remember correctly.
How I use the honey tree is to go out and put honey on as many tree as I can and hope to find what I want.