The alarm went off for a long period of time now remote battery went dead and system wont activate

SOURCE: 1998 Camry, turn ignition to On kills electical system

This is a Direct Fault Caused by the Alarm System Starter Kill. Do you have an Alarm Override Switch???? You may need the Dealership to Reset the Alarm if not.

SOURCE: central locking not being activated by remote

somehow the car when on valet mode, go to a alarm shop , they should be able to re arm your car without to much damage to your pocket, or read your cars manual, it might inform you on how to fix the problem.

SOURCE: My car alarn went off and now we can not start our

If the alarm was on for a long time, your battery might be drained. If so, recharge.

SOURCE: 1998 Camary security system

See this excellent write-up on toyotanation.com below:
http://www.toyotanation.com/forum/t96974.html

It describe in details to program stock or aftermarket replacement remote. It covers all models, so just make sure you know what the FCC # on your remote when you look up this DIY.

SOURCE: i have a 1994 toyota

Hello. Welcome to FixYa. Please allow me to assist you. If you have a factory alarm system (not one that was added from a non-Toyota alarm manufacturer), the way to disable the alarm is to insert the key into the ignition, cycle the key from lock to on (not to the start position) five times. Try that and see if that fixes your problem. Remember, this trick will not work if you do not have a Toyota system installed.