<p>My realtime app generates a data log: 100 words of data @10Khz.  I need to analyze it and produce some plots of the results.   There are intermediate calculations involved - I need to take some differences, averages, etc.   Excel would work fine, except for:</p>

<ul>
<li>the 32000 item limit on graph data series is too small - that's only 3 seconds of data.</li>
<li>the glacial speed at which it processes changes to graphs containing large data series is unbearable.</li>
</ul>

<p>What are good alternatives to Excel for manipulating and plotting large quantities of data?  I'm looking for something interactive, not a library. </p>

For this sort of stuff we typically roll our own, but I know that isn't the solution you want. Can you use a good quality database (eg Oracle) to do the manipulation, then maybe put the summarized data back into Excel for the plotting? I believe Excel will link to databases these days, so you could make it quite automated.
Otherwise there are statistical tools like [SAS][1], but get your cheque book out first.
[1]:
http://www.sas.com/technologies/analytics/statistics/stat/index.html
SAS