With the assumption that you will likely be undertaking similar endeavors in the near future I think a different approach is required than what has been proposed in previous answers. I would like to suggest that you outline and establish a strategy for "securing" future applications/systems. By using a strategy you can ensure consistency, delegate responsibility and improve your practice over time.
I believe that securing a server shouldn't be done in an ad-hoc type fashion, but rather methodologically and consistently. It should be a repeatable process with as little room for mistakes as possible. Us humans are notoriously bad at remembering details, often blending bits of information into something entirely different.
In the scenario you describe above using a perspective of Availability seem to be mostly relevant and useful. Begin by describing establishing system dependencies. What other systems are required to be accessible in order for the application to function? Do you depend on an external user directory? Dependencies are important because they help to better understand potential "avenues", or vectors, of attack.
Next flesh out details of exactly who should have access to the system and the primary access "terminal" (remote desktop, workstation, laptop, mobile phone etc). By doing this you'll have begun to establish your frame of reference, or system boundary if you like.
It's very likely that there are organizational limitations that you simply need to obey. These might include company mandated authentication methods, encryption algorithms and such, describe and document these limitations. You might also have to consider legal requirements, and now might be a good time to find out.
Once you've established the more "fundamental" building blocks of your system, it's time for some creative brainstorming. Try and describe all potential avenues through which you (or an attacker) could access the system using the above system description as a sort of limitation.
What you'll have to do next is determine what security controls would assure the most appropriate protection. Yes, I know, this is where things get complicated because it's a somewhat subjective process but regardless necessary. Every countermeasure you determine is necessary will be associated with a certain cost (time to install, configure, maintain and eventually retire).
You'll also want to try and describe with some sort of quantitative measure how "well" a collection of countermeasures mitigate a particular risk, or "limit" an avenue of attack. I believe this to be important especially for "upper management", speak a numbers language. For example, a "good" implementation of salted passwords will entirely eliminate the threat of precomputed hashtables and could hence be described as a "high assurance" countermeasure.
- Determine primary security goal/target (confidentiality, integrity and availability)
- Establish system dependencies
- Who, how and when?
- Detail organizational and/or legal requirements/limitations/constraints
- Brainstorm attack vectors (guess you could call this a lightweight threat analysis)
- Choose countermeasures appropriate to the system in question
- Make rainbows, colorful charts and unicorns.