Currently there is a bugger in the bot-left base, but should get towers there (and vendor i thinx) in next version.
Most base bonus are the units that you receive when you claim it.
Torture Chamber offers a key which can be used to release the creeps in the Torture Chamber.
Garden of Edin gives a special Water Protector tower.
Water-fall base (above the Hold) offers a special tower as well.
Abandon town comes with repairers already built.
The Pirate-base (Bot Right) comes with awesome pirate units, and has a quest similar to Mr. Shinkel.
This is all from my memory and not meant to be 100% accurate, as there are probably more stuffs I don't even know about yet, 6.45 has many changes. If you play around for awhile with different places it helps. You're only allowed 1 initial base claim, but the science lab will still give you bonus when claimed the 2nd time. But you won't receive the Water tower or Protector from Garden of Edin or Water-fall base unless its your first claim. <it always helps to have a plan>