Hi Johnny,
Well I can answer this question from my real world experience being both a PMP certified implementer of enterprise software solutions as well as an experienced Agile PM having managed a team of 14 in a Hybrid Agile software development project.
When implementing COTS (commercial off the shelf) software I find that the PMBOK can be followed quite closely. If followed to a "T" the PMBOK will steer you down the path of a "Waterfall" methodology. If you are not familiar with Waterfall, this is the approach where most of your project time is spent early in the project gathering requirements, performing design, estimating, etc. Build or development comes much later in the process. The reason this approach works well for software implementations is because the customer generally wants to know the cost upfront for the project. The only real accurate way to determine the project cost is to follow the waterfall approach...at least initially.
The Agile/Scrum methodologies work much better for building software. When I say build I mean the entire build process from design, development, testing, etc. I won't go into the differences between what is covered in the PMBOK, Waterfall or Agile methodologies as that is not what you asked. Agile is very much about iterative design & build, and less up-front design. In agile you want to iterate quick, and perform JIT (just-in-time) requirements gathering (using storing), design, build and testing (TDD). This reduces the amount of waste and produces usable software earlier in the project. Agile has many benefits to software development projects.
Now what I have found helpful is taking the waterfall approach as far as you need to build an accurate estimate and resource plan. Once that is complete you can switch in more of the agile processes to finish off your project.
Remember not to confuse the PMBOK with an methodology. PMBOK is a set of industry standard processes that can be followed to deliver a project; not just a software project, it could be engineering, municipal planning, etc. There are many parts of the PMBOk that are beneficial in the software development world such as: communication planning, risk planning, project close-off, etc.
It's a pretty broad subject so I hope this helps you make the appropriate decision for your project. Remember one size does not fit all.