General "smallness":
* mini- (e.g., minivan, mini-skirt)
* micro- (e.g., microscope, microbe)
* small- (e.g., small town, small talk)
* little- (e.g., little boy, little finger)
Specific types of smallness:
* sub- (meaning "below" or "less than," can also denote small size) (e.g., submarine, subatomic)
* nano- (extremely small, often referring to the billionth part of a unit) (e.g., nanotechnology, nanoseconds)
* demi- (half or partial, can imply a smaller size) (e.g., demi-tasse, demi-god)
* petti- (small or minor) (e.g., petticoat, petty cash)
Other prefixes depending on the context:
* short- (e.g., shortbread, short story)
* thin- (e.g., thin film, thin slice)
* light- (e.g., lightweight, lighthearted)
The best prefix to use will depend on the specific word you are creating and the specific meaning you want to convey.