I think it depends on your needs. Perl's pretty good at splitting and joining, so I don't think you're going to run into a problem if you stick the whole chunk of data (as a string) into a single column.

I certainly wouldn't have 1,000 columns in my database table, no...

If you really want to store the values separately, then I'd turn the problem sideways and store each into a separate row, rather than a separate column.

Example: Let's say you've got a user with user ID 332. In the first version (one column), you'd have:

KEY   VALUE
332   1,4,2,4,1,6,4,6,5,1,0,...
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In the multi-row version, you'd have:

KEY   VALUE
332   1
332   4
332   2
.
.
.
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If you need them in a particular order, you could add a column to order against:

KEY   FETCH_ORDER   VALUE
332   1             1
332   2             4
332   3             2
.
.
.
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and then retrieve them with:

SELECT VALUE
  FROM MYTABLE
 WHERE KEY = ?
ORDER BY FETCH_ORDER ASC
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