Is fsck just taking a long time to run, or is it dropping you into a terminal shell with instructions to "run fsck manually?" If your problem is the "terminal shell/run manually" one, then the "quick check" run by fsck when the system boots has found some errors in you hard drive(s), and you really need to fix them before proceeding. So you should just run fsck manually to correct any errors it finds. (If it can -- sometimes the errors are that the drive is failing and needs to be replaced.)
On the other hand, if you're complaining that the "quick check" is taking too long, it may just be that fsck is running a "complete check" instead of the usual "quick check." Typically, when you create an ext2 or ext3 file system, fsck is told to run a "complete" check every 20 or 30 times the file system is mounted. (You can change the "complete check" frequency with the tune2fs command.) Let it run to completion and you should not be bothered by fsck until the next "complete check" is run.
Of course, if you have a few hundred partitions attached to you system, even a "quick" fsck can take a long time. But, if you've got that much hardware attached to you system, you really need to read a good book on Linux system administration or take some classes on administration.
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