I'm a fan of Bartender. Never tried Bongos, but I never felt the need to. To me, configuring Bar3 is unobtrusive and easy. Being able to lock/unlock bars with the click of a button, and being able to shift-drag stuff when it is locked just makes my day (makes swapping a ditching quest items for dailies on my bar easy as pie).
I also have a macro to show/hide two bars that I often use in town or at the beginning of an instance (such as portals, mage table, professions) that I want to be able to access quickly, but do not want them crowding my interface normally.
Most of this may be do-able with Bongos as well, but like I said, I've never had a reason to switch.
I have debated using flexbar though.. one of these days I might try them out and just go crazy with putting buttons all over.
Edit:
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Spells and Macros can be all assigned keybinds, without needing them to be on an actionbar. (replaces spellbinder-type mods)
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I also do this with bartender, I just have one bar with a few keybinds and macros and have it set to hidden.