Custom chips are designed by a company for a specific product, the alternative is "off the shelf", where a company buys in chips designed by another company.
The Amiga's chipset was custom designed for the Amiga, it's CPU was an off-the-shelf part made by Motorolla for general sale.
That is kind of what I am getting at though. Like psxphill said, some custom chips are good, and some are not.
There is no value to users in having a chip custom. Being the only system running the chip does not increase the performance of that system. The 'Custom-ness' of the 'custom' chipset did not improve the Amiga in any way. It was the 'coprocessor-ness' of the 'custom' chipset that made the Amiga shine.
This misunderstanding of why the Amiga chipsets where good lead many Amiga fans down a self destructive path. They start obsessing on having the system 'custom' for custom's sake because they have come to believe that custom = good and cots = bad.
With all other things being equal, cots > custom. The only time that custom is a better choice is when it brings something to the table that out weighs the cost benefit (for manufacture as well as further R&D) of using cots parts. The fact that the Amiga had a 68k showed that Amiga understood this.