The Basics
For starters there is the Quick Start manual.
Logix5000 Controllers Quick StartIf you don't deal with the PLCs or RSLogix 5000 too much and just need a quick reminder about the hardware or programming then the System Reference is perfect.
Logix5000 Controllers System ReferenceThe Essentials
If you are getting into programming and designing a system then you'll want to start off with the Common Procedure Manual. It has a lot of helpful examples dealing with all aspects of the system. Logix5000 Controllers Common Procedures Programming ManualNext comes the nitty gritty of each instruction. It's a good idea to at least peruse all the instructions so you have an idea of what is available.
Logix5000 Controllers General Instructions Reference Manual Logix5000 Process Control and Drives Instructions Reference Manual Logix5000 Controllers Motion Instructions GuardLogix Safety Application Instruction Set Reference ManualAn often overlooked manual but filled with great information for getting the most out your designs is the Design Considerations Reference Manual. Certainly a must read if you are knee deep in the development and programming of Allen Bradley PLCs.
Logix5000 Controllers Design Considerations Reference ManualHardware Specifics
Specifics for the hardware can be found in the User Manuals and Installation Instructions for the PLC.ControlLogix
ControlLogix System User Manual ControlLogix Installation Instructions ControlLogix Controller and Memory Board Installation InstructionsCompactLogix
CompactLogix System User Manual CompactLogix 1769-L31 Installation Instructions CompactLogix 1769-L32E, 1769-L35E Installation Instructions CompactLogix 1769-L32E, 1769-L35E Installation Instructions CompactLogix 1769-L32C, 1769-L35CR Installation InstructionsFlexLogix
FlexLogix System User Manual FlexLogix Controllers Installation InstructionsSoftLogix
SoftLogix System User Manual SoftLogix Controllers Installation InstructionsGuardLogix
GuardLogix Controllers User Manual GuardLogix Controllers Installation InstructionsNetworking
If you are deciding on which network to use then see the Design Considerations manual and the section "Determine the Appropriate Network". Otherwise, for existing networks the following are helpful.Ethernet/IP
Ethernet Design Considerations for Control System Networks EtherNet/IP Modules in Logix5000 Control Systems User Manual Guard I/O EtherNet/IP Safety Modules User ManualControlNet
ControlNet Modules in Logix5000 Control SystemsDeviceNet
DeviceNet Modules in Logix5000 Control Systems User Manual Guard I/O DeviceNet Safety ModulesThe links are from the AB site so they are the latest and greatest manuals. Let me know if any of them are broken or if I forgot one you think is essential.