The CY8CKIT-050 kit is a PSOC5 dedicated kits and has onboard programmer/debugger. it is the most simple to use of all the kits but it only supports PSOC5.
The CY8CKIT-001 kit is more flexible. It supports 3 types of devices (PSOC 1 , 3 and 5LP). comes with plug-in mcu modules for the 3 types of devices and also includes a Miniprog3 programmer/debuger. To use it you have to plug-in one of the included mcu modules and the miniprog3 to the base board.
If you can aford it I would recommend the CY8CKIT-001 kit as it includes a miniprog3 that can be used to program external devices and supports all cypress devices.
... and cypress told me there will be a PSoC4 processor module, so the Kit-001 will be able to support *ALL* PSoCs.
I admit: I have got both Kits. When you start with the -50 kit there is no money thrown away when later on you decide to by a -001. As a mattert of fact: many projects include communication between two processor-boards via I2C, SPI or another protocol. So when owning two PSoC Kits you will be able to develop and test for those projects easily.