We just went through this exact same exercise at the company I work for. When our antiquated, poorly-designed MRP system started causing too many headaches, we carefully counted the cost of moving to something like Salesforce.com or SAP, but ultimately ended up writing out own system from scratch. After running the two systems in parallel for 6 months to ensure the new system had data integrity we were comfortable with, we cut it off. Having just closed our first month "live" on the new system, I must say it's a real breath of fresh air for both the IS staff and the rest of the company. Gone are the days waiting for the slow moving MRP company to update their slow system to add features or fix bugs for us. Our hands were tied with the old system, and now the door is open to all sorts of possibilities. People are constantly saying "wow, we can do xyz now!" or "this wasn't even possible before with the old system". The daily complaints about the old system have been replaced with daily feature requests and positive comments.
The small team that built it remains on staff, and if something doesn't work, we fix it. If someone requests a feature that makes sense to the overall design goal, we sketch it out, schedule it, and implement it. We carefully weigh everyone's feature requests and implement only those that make sense for the overall "greater good" of the system. That way we keep feature creep down while building something that helps people get their job done faster. In the time between bug fixes and feature request, we are constantly polishing the system to make it more efficient. We now have a DEV environment where we can test out new ideas and features and release them to production only when they are ready.
Since we built ours with FOSS technologies, it's been a joy to integrate with our other trading partners (suppliers, our web store shopping cart, etc). The money we are saving on not having to pay for licensing costs (recurring yearly, never ending), we have invested in hardware and infrastructure to run the new system.
Perhaps the biggest benefit is when the system is released, the company will have a team on staff that knows the system inside and out, because they built it.
I would highly recommend any company considering buying an out-of-the-box ERP system to consider having an in-house team build them a custom solution. With the right group of developers, it can be a really rewarding experience for everyone!