The first one is RTS+DTR: RTS controls RESET or CH_PD, DTR controls GPIO0 — this one will be enabled by default in the next release.
The second one is DTR+TXD (see schematic posted in this thread: https://github.com/esp8266/Arduino/issues/22).
If you have something else in mind, please open an issue against esptool-ck and I'll implement that as well.