There's rarely a dipstick for the manual transmission, so when you're doing other lube work, remove the fill plug for the transmission and see if it is filled to the bottom of the fill plug hole. Drain and refill the transmission at least once every two years, using only the specified lubricant. Some gear oils will not adequately protect some of the metals of a transmission, or are too thick for smooth shifting.
Many modern transmissions specify the use of multi-viscosity motor oil in the transmission. If that's the spec for your transmission, just be sure to use the proper viscosity. Some manual transmissions recommend year-round use of Automatic transmission fluid (ATF), though it may protect as well as gear lube during hard summer-time use (some users may switch seasonally, on their mechanic's recommendation). Use the right fluid, or transmission shift quality will suffer.
Rear axles with limited-slip differentials use a lubricant with a friction modifier to prevent chattering around slow corners. Compare the label on the container with your Owner's Manual recommendations.