How to clear CPU congestion?

.
My system cruises along fine for days without any CPU overload
('top' normally shows CPU usage at about 2%) ... and then something
happens (I don't know what) that causes the CPU% (as shown in the
'top' results below) to shoot up to 90+%.

How can I figure out what causes this aberration?
And is there some way to unclog it without having to reboot?

top - 12:17:28 up 7 days, 50 min,  3 users,  load average: 2.08, 2.08, 2.25
Tasks:  87 total,   1 running,  86 sleeping,   0 stopped,   0 zombie
Cpu(s): 50.7% us,  4.5% sy,  4.9% ni, 39.6% id,  0.1% wa,  0.1% hi,  0.0% si
Mem:    515484k total,   447644k used,    67840k free,    78252k buffers
Swap:  2096440k total,    79664k used,  2016776k free,   130016k cached

  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
 3098 root      25   0 80492  62m 4460 S 98.9 12.5   5233:50 X
    1 root      16   0  1560  480  460 S  0.0  0.1   0:01.76 init
    2 root      34  19     0    0    0 S  0.0  0.0   0:00.34 ksoftirqd/0
    3 root      10  -5     0    0    0 S  0.0  0.0   0:03.16 events/0
    4 root      10  -5     0    0    0 S  0.0  0.0   0:00.01 khelper
    5 root      18  -5     0    0    0 S  0.0  0.0   0:00.00 kthread
    7 root      20  -5     0    0    0 S  0.0  0.0   0:00.00 kacpid
   81 root      10  -5     0    0    0 S  0.0  0.0   0:00.47 kblockd/0

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