Occasionally in the WordPress world you come across plugins that just aren’t tidy. One of the nasty things that can happen is that your wp_options table gets filled with transient entries that are never garbage collected after their expiration. If you have a relatively high traffic site, like jMonkeyEngine, this will slow down your site to a crawl especially if new entries are being made on every page view (not naming names but the appropriate developers know the issues if they check their forums).
That said, there’s a pretty easy way to just get rid of all the transient entries in your table regardless of expiration.
Run this if you notice your wp_options table is becoming bloated, or better still, deactivate the suspect plugin.