This is my Arduino built using a ATMega328P w/bootloader on a protoboard. In the upper left is a USB to 5 volt TTL serial converter hot-glued to the base. This provides send, receive, and reset along with +5 volt and ground. Being already on a protoboard makes it much cleaner to connect various other devices.
Here is the hookup for this unit. Many designs like this do not include the diode (1N914 or almost any other diode). Without this you get a 10 volt spike on the Reset line at the trailing edge of the DTR pulse. Not good.
Also notice the lack of the 2 capacitors that most people show on the xtal connection. These are only needed if you need VERY accurate xtal frequency when running in a parallel resonant mode (as most micros do). They are not there to 'help it oscillate' or to 'protect the xtal'. The difference is a few parts per million if that really matters to you.
The 10uf capacitor is provided for good practice. It keeps the voltage stable when 'who knows what else' may be plugged into the protoboard. Especially true when loading bootloaders into other micros.
You can get the same functionality by just using an Arduino Nano plugged into the protoboard.
Either way, this is one damn handy setup when used with a 4 channel oscilloscope. Especially when doing initial experiments with new parts.