Some useful links and scripts ...

http://java.sun.com/javase/6/webnotes/trouble/other/matrix6-Unix.html has some very useful info on how to debug java applications deployed on Linux/Unix.

Also, here is a little script which would dump all system stats as well as stats for processes owned by user -

#!/bin/sh

TERM=vt100
export TERM

LOGDIR=./

time=$(date)
min=${time:14:2}
today="`date +%m%d%y`"

FNAME=$LOGDIR/$today
# echo $FNAME
# exit 0
touch $FNAME

echo "______________________________________________________" >> $FNAME
echo "               $time" >> $FNAME
echo "______________________________________________________" >> $FNAME
echo "**************** TOP *******************************" >> $FNAME
top -b -n 1 >> $FNAME

#
#  Get every socket out there, resolve IP addresses, and print which 
# process has that socket open
#
echo "**************** NETSAT *******************************" >> $FNAME
netstat -ap >> $FNAME
echo "**************** Process Status *******************************" >> $FNAME
ps -auxww >> $FNAME

#
#  How much memory are the processes using?  This will be a percentage
# of the total.
#
echo "**************** Process MEMORY Consumption ************" >> $FNAME
ps aux | awk '{sum +=$4}; END {print sum}' >> $FNAME

#
#  A busy system will have the kernel use up a lot of memory.  But, the 
# +/- buffers/cache entry should show free buffers if not, then we have 
# memory issues.
#
echo "**************** FREEMEM *******************************" >> $FNAME
free >> $FNAME

echo "****************************************************" >> $FNAME

#
#  Get all the  processes and then find their open sockets.
#
#
echo "****************  OPEN SOCKETS ***************" >> $FNAME
/usr/sbin/lsof -p `ps -u root -opid | grep -v PID | awk 'sub(/^[ \t]+/, "")' | awk '{ str1=str1 $0 "," }END{ print str1 }'` >> $FNAME
echo "****************************************************" >> $FNAME

echo "               $time" >> $FNAME
echo "**************** END *******************************" >> $FNAME
echo "****************************************************" >> $FNAME
exit 0