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well, the clicking noise can only be one of two things in an external enclousre, the drive or the cooling fan. If it was the fan, then almost assuredly it would be constant or move from a clicking to a loud, constant noise as the fan sped up. So, let us move to it being the HDD itself.
Generally a clicking noise in the HDD is a head crash, meaning the read head of the drive is crashing into the platter. This is bad news and not something to mess with often, if there is data on the drive you need and have not backed up. There are several TEMPORARY fixes you can try if you need to attempt to recover some data. One suggestion is to put the drive in a sealed ziplock bag and stick it in the freezer for about 15-30 minutes. This has worked for me exactly one time, and only let the drive run again for about 20 minutes, which let me save some of my MP3s. If it is a head crash, every time you turn it on and it clickcs against the platter, you are permanently destroying data (scratches to the platter are not recoverable). Many newer drives will detect a read-head collision and stop the platter from spinning, which is why it may not continue after a few seconds.
Redjake has some good steps for troubleshooting, but noises + hard drives is generally a pretty unfixable issue.
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