Good advice here, I'll just add:
Think of the 3.0 as the upscale, better built Miata, the Si as the upscale, better made and more luxuriously appointed S2000 and the M as the Boxster fighter and you'll get the idea.
The 3.0 is probably the best daily driver - 17 inch wheels and tires
will offer a better ride and the slightly smaller (detuned) engine good gas mileage.
The si will be a bit more harsh and the wheel/tire combo of 18's more fragile (some come with 17's) but otherwise a good DD
The M is in a different class - it's a lot of power for a lightweight sport car and the gas milage really suffers. However, it's the highest performer of the three, but that's academic, you'd only exploit it at the track, and you'd need a LOT of talent to exploit the M's capabilities well.
IMO, either the 3.0 or Si would give you more than enough handling and thrills for street driving, return good mileage and be comfortable and livable for everyday driving.
Your choice, go drive'em and enjoy.
PS: pre 2006, the Si was the 3.0 and the 3.0 the 2.5.