When using IDA Pro, there are a number of features that can be used to make reading the disassembled code far easier - renaming variables, defining data structures, colouring blocks of code, moving blocks of code about (in addition to the graph, which is very useful).
If you use a conventional disassembler, this isn't available.
Traditionally, I would use a combination of printed out code and pencil along with annotated text files to analyse the disassembly, but I feel this is a long way from what IDA Pro provides.
Are there any tools to make this job easier? I am not looking for alternative graphical disassemblers to IDA as there will always be times when you are limited to the output from tools such as objdump or proprietary command line utilities.