Sorry for the confusion. Apparently on OSX the program I'm asking you to run is called Activity Monitor. This allows you to keep track of which programs are using what percentage of your CPU and memory. Running this concurrently with Minecraft will let you see if there's increased CPU or memory use going on when these issues crop up. That's what I meant by register. Run Activity monitor while playing Minecraft and see if anything is changing when this happens.
If nothing registers as happening on your computer in Activity monitor, then the problem is either in the way MindCrack's combination of mods interact with the JAVA Virtual Machine for OSX (which if this was the problem could possibly be fixed by using an older or newer version of Java, as I suggested in the prior post) or the problem is on the server you're just feeling the consequences on your computers. It's possible the server doesn't have enough RAM allocated based on how people are using it, and this is just the manifestation of that. You may want to allocate a bit more RAM to the server in this case. You could also try to find ways to reduce the amount of RAM your server needs - if people are using chunk loaders or world anchors or running lots of quarries, ask them to disable them for now and see if the problem disappears. If it does, gradually reintroduce them unt il you find a happy balance. If people are using a lot of BuildCraft pipes to move items, see if disabling them temporarily fixes the issue. If it does, look into replacing them with routers from the Factorization mod and/or Tesseracts from Thermal Expansion - those seem to cause a lot less lag on my server. You also may want to consider replacing BuildCraft energy pipe with Thermal Expansion's Redstone Conduit - it also seems to cut down on lag. Mob spawning also eats up a lot of CPU and memory - you may want to set the game on peaceful when you can.
I've noticed too on my server that a lot of times other people are often feeling the consequences of what one or two other people re doing and so lag spikes seem random if you don't immediately ask everyone what they're doing when one happens. If people are flying or using powered rail to go everywhere quickly and often, this can cause all kinds of lag - ask them to use linking books from Mystcraft instead and use a link modifier to enable intra-linking and following on the books - these are much faster and don't really cause noticable spikes.. If one person is exploring ungenerated territory then this can cause enormous lag spikes. I like to go on expeditions with everyone on the server when we're going to generate new territory, that way everyone is causing their own lag and we get to have fun in the process. And while linking books from Mystcraft can solve problems, the new worlds that Mystcraft generates can make some servers stop and kick everyone off until it finishes the initial world generation. Especially worlds that use the "Cave World" generation option.
You can also try running the "/debug start" command, allowing a few minutes of regular gameplay to pass, and then running the "/debug stop" command. You'll get a basic reply in the console saying how many ticks you got in what time. Divide the number of ticks by the number of seconds to get the ticks per second. The ideal is 20. Nobody gets 20, but that's the ideal. If it's extremely low, though, like 2 or 3 ticks/second, then something is generating a lot of lag on your server. You can view a more detailed output of your debug in your server's /debug folder. Looking at it can sometimes help you pinpoint where lag problems are coming from.
I know this reply was everywhere, but I'm just trying to think of anything that may help.
Oh, one other thing. I had a user who had this exact same problem and the culprit was Forestry backpacks. This is a long shot, but do you guys use those a lot? Try putting them in a chest and walking away and see if your issues suddenly disappear. It's definitely not something I would think of, but I know it solved the issue you're describing with someone else.
