I am about to go through every plugin we are using and testing it. Here are some issues I have run into, just FYI:

• HeroChat is in some kind of war with some Brazilian MC server, DDOS, flamewar and all. The current version of Herochat seems to work fine so far however. I will continue using that.
• BringBackTheEnd is broken and there is no update of the admin whatsoever. Either we manage to find a new one or we have to stick with once-a-day resets of the end.
• iConomy is abandoned, and seems we are only lucky its still working since some other server have seen major issues in accounting accuracy. Since we do not use this plugin together with other plugins, we can replace it with our own code instead. Other plugins out there do not support MySQL so we are stuck on that. Once we would want to charge for other stuff than buying/selling, we would need to find a plugin that interfaces with those plugins however. I will continue running the current version until I have time to rewrite the basic functions we are using in PHP.
• MapMarkers is abandoned since long but working fine. Should not be an issue since dynmap creates a similar file we can use. I use it to display the users on the 2D map
• NoCheat+ is not released as a final version yet. I will try to install it and if there are issues, simply disable it for the time being.
• Whitelist is abandoned since over a year but has been running fine. Now mincraft added finally a command to reload the whitelist file in case it has been updated externally so we can phase out the plugin. I only have to add the reload command when someone has been whitelisted and we are good to do. Will do after upgrade.
• WorldGenerationControl is used to forcibly generate regions no-one has been visited yet, after map enlargements etc. It seems abandoned but still working fine. Dynmap has a similar function just in case.
• c10t seems to be abandoned since some time but receives sporadic updates. I use it to make the 2D map. If they do not update, I wrote a script to assemble the 2D maps from dynmap into such a map, and I can re-activate that.

All other plugins either have updated to 1.3.1 or have not but also seem to be working just fine with the recent versions. I will test the updated versions now and then see if I run into issues. Protection and the possibility to run all worlds with no issues between them is the first priority. Economy & Shops is the second etc.