Auto transmissions go out all the time. It's a fact of automotive life. After a good number of years and miles, they just start to break down. For manual transmissions, there are certain signs that make the inevitable a bit more predictable in terms of identifying when a transmission will go bad.
Drips and Leaks
Transmission fluid, reddish in colour, doesn't belong on the cement below your vehicle. If you have a transmission leak that is really obvious, at the very least the gaskets between the transmission casings are bad and need replacement. Worse, many leaks are caused under pressure and signal transmission assembly problems. Too much leaking and you lose valuable lubrication, which then causes parts to grind.
Pay Attention to the Clutch
The manual transmission clutch is probably one of the most abused parts on an automotive manual transmission. This component is basically in charge of engaging and disengaging your engine gears as you change speed. As a result, it is used constantly, put under pressure, meshed, un-meshed and sometimes made to work at the wrong time due to driver error. When the clutch starts to go bad, it will become very evident by two major behaviours: failure to stay in gear and failure to engage higher gears (i.e., fourth or fifth gear).
Not nearly as common as a clutch failure, a lower gear failure can occur if the gears have been damaged or chipped badly. Usually this happens when old gears a suddenly jammed badly. Something breaks and then the gear basically begins to miss its teeth meshing properly. It will feel like your front tire is going flat with a rough driving and bumping/jerking feeling.
Clanging Noises While in Idle
When things get loose in an engine, they make it pretty obvious, and transmission parts are no exception. Loose gears and clutch parts are going to start banging against each other when sitting still but still being vibrated by the engine churning over. The noise will go away as the engine engages and you drive, but eventually other problems will occur due to the loose parts.
Difficulty or Inability to Shift
If you know the clutch is good, then difficulty or a complete inability to shift means very likely that your transmission transaxle assembly has gone bad. Sometimes this is caused by bad synchronisers in the assembly and not the gears themselves. However, in most cases a transmission rebuild is required to fix the problem.
A Bad Shift Lever
One of the weirder but common symptoms to watch out for after 80,000 miles is a worn shifter. While not really being part of the transmission, it affects your ability to work the clutch when the clutch pedal is pressed. Many times a small ball in the shifter assembly breaks down and crumbles, making shifting horrible and prone to popping out of place. Again, a rebuild and replacement is usually the fix for the shifter assembly.