I am using the latest dev of Bukkit and what I did was enable the new auto save feature. The default save time is 400 ticks or 20 seconds. I have a large server and at peak times I have 80 - 100 users on and I was noticing massive lag spikes every min. It took a couple of days of playing with plugins until it clued in that it could be the fact that the server was saving twice a min. I changed it to 12,000 ticks or 10 min and everything is running perfect now. I know alot of users arent using the dev versions or are using other save plugins but for the few using this feature if you are having lag spikes - check out your bukkit config