First, run the following as root to find out which folder is using the most disk inodes:
# for i in `ls -1A`; do echo "`find $i | sort -u | wc -l` $i"; done | sort -rn | head -5
94520 usr
40694 proc
39851 mnt
39845 srv
34830 home
Continue to recurse through folders until you are able to find the offending files/directories causing the high inode usage, and delete.