If you're looking for pre-pakaged apps and tools, there are a ton of them, but I can't give many recommendations. If you're more of a do-it-yourselfer, and want to get into scripting, you can do just about anything you want through WSH, ADSI, and WMI.
As a specific example to address one of your issues, here: http://pubs.logicalexpressions.com/Pub0009/LPMArticle.asp?ID=68 is a script to find old, unused computer accounts. A little research could modify it to do the same for user accounts.
I'd also recommend installing and looking over the Windows Support Tools and Windows Resource Kit Tools. Lots of stuff of varying usefulness, depending on your needs and requirements.
Overall, there are advantages to either way of doing things; the off the shelf software way is easier, but costs more. But whichever route (or combination of routes) you choose, you definitely need to manage your network. Good for you that you see the need starting off; bad for you it was left for you in such a mess. . . .
On the subject of old user accounts, our policy is to disable an account immediately on employee separation, but not to delete it (or their mailbox) for 30 days. In cases where there may be reasons to hold onto it longer (i.e. legal issues, grievances, anything that might bite you later), keep it disable, but keep it, until you're sure you don't need it. Most of the time, that's not an issue. . . .