Though you have plenty of input:
I've sort of standardized around 0603 parts because they're a nice mix of inexpensive, small, and still fine to work with by hand. LEDs tend to be just a bit more challenging than other parts of the same size (usually the pads on the end are a tiny bit smaller and you always have to remember how their polarity is marked on the top side

), but are still plenty doable by hand. You run slightly higher risk using smaller and smaller parts in that you can't heat them for as long while soldering, but honestly, it's pretty rare that you have to apply heat for very long to an SMD part, and I can't remember the last time I burned out something 0603 with just the iron.
For indicators, I also end up using 5mA or less, usually... and blue/white LEDs, with their much higher voltage drop, often need considerably less to not stick out like a sore thumb. Red/orange LEDs are great for low voltage, low current operation, but sometimes you just need more than one color.