apply() and call() cause a huge slowdown.

Strange - after fixing that bug you reported, your code doesn't work at all. myEve ends up containing:

{
      "agents":{
        "0":{
          "RPCfunctions":{},
          "init":function () { ... },
          "add":function (params,callback) { ... },
          "sendMessage":function () { ... },
          "sendMessages":function () { ... },
          "agentName":"0",
          "options":{},
          "send":function (destination,message,callback,messageId) { ... },
          "publish":function (topic,message) { ... },
          "subscribe":function (topic,callback) { ... },
          "unsubscribe":function (topic,callback) { ... },
          "schedule":function (callback,time) { ... },
          "repeat":function (callback,time) { ... }
        }
      },
      "topics":{},
      "callbacks":{
        "0":{
          "6qyhirtqklq8":function (answer) { ... },
          "4ec0vmqv6pa8":function (answer) { ... },
          "5k462y63k7pc":function (answer) { ... },
          "58ich9zfwlo":function (answer) { ... },
          "1a8nici2pqxs":function (answer) { ... },
          "5vrmbdrmbh4w":function (answer) { ... },
          "5hu6aackwwow":function (answer) { ... },
          "4u7kbc25iydc":function (answer) { ... },
          "2zzm7mn6g8sg":function (answer) { ... },
          "6jg883hgcscg":function (answer) { ... },
          "3gmwt7ql81hc":function (answer) { ... },
          "5r67qpludmv4":function (answer) { ... },
          "lvvbuu47tio":function (answer) { ... }
        }
      },
      "transport":{
        "ANT":{}
      },
      "receivedMessages":[
        "7rzs33b908s",
        "6tbna54x2lq8",
        "2zj7n5cd77cw",
        "24hfsn1bgj9c",
        "6130s6ugog00",
        "6tjbyw7a38xs",
        "34ydibjauu9s",
        "5pdp63lci680",
        "7242cassfuk",
        "1aj6hevntsgw"
      ],
      "messageHistoryLength":10}

By the way, I noticed a callbacks.lenght on line 120 - but that's not the problem.