In order (may miss some as I've not used all mods) of best to worst, simplest to most laborious setups.
Best most simple way to automate Apiaris = Extra Utils transfer nodes/pipes
Then EnderIO which are kinda most complicated to setup
Then BC pipes
and lastly TE which tbh I found completely useless and buggy and ended up losing bees no end (will never use these again).
So an explanation as to why I say EXUt are the best, they are because of one very simple factor and that is you can whack the pipe with a stick and set direction. So you don't have to mess about configuring the extract or insert in any way shape or form it simply pulls out the produce/bess and inserts the bees on a first come service so don't use for breeding only for production. Then the rest hit the one-way system and head for the storage area. A bit like using iron pipes, so simple, easy to setup, can't go wrong (which is important) and is a system you can 110% rely on and from someone who does bees, bees, bees and more bees a LOT trust me I know.
EnderIO are pretty good but nowhere as easy to setup as ExUt system.
BC is old and messy with gates and stuff.
Lastly if you're still playing 1.6 and below I would suggest that you never ever use TE itemducts, I had one very bad experience with them and lost my entire set of production bees due to the pipes throwing the bees out of the system.