If you are planning to use the TI's CC25xx series you have two choices - use the CC2540 or the CC2541. We have attempted to list out the difference between the two.
1. No Support for USB in CC2541
The CC2541 removes the support for USB as compared to CC2540. It instead, introduces hardware I2C on the same pins. So, if you do not plan to use USB, the CC2541 could be a better choice, but you should also look into other differences as well. If you are using I2C, this could be another reason why to prefer CC2541.
2. Higher Transmit power in CC2540
The CC2540 has higher transmit power at 4 dBm compared to 0 dBm in CC2541. The CC2540, should therefore have slightly better RF performance in terms of the range of radio.
3. Higher Power Consumption in CC2540
The higher output power in CC2540 comes at the expense of more power consumption - it consumes 27 mA when driving 4 dBm transmit power as compared to 18.2 mA in CC2541 when driving 0 dBm power.
Additionally the receive power consumption in CC2541 is marginally lower at 7.9 mA versus 19.6 mA in CC2540.
Other than the differences listed above the CC2541 is pin to pin replacement for CC2540. It can be substituted and all circuits, except the USB / I2C differences as noted above.
Note that TI has a more recent CC26xx series that is better in terms of power consumption has faster ARM Cortex M3 processor. You may want to check the difference of CC26xx with CC25xx here