There is no "should" about it; the choice is yours. Choose the product that best suits the criteria you have decided it must meet.
It may be possible to take existing open source software and add your own programming and admin skills to come up with an application that would cost you far less than a proprietary product. Setting up a departmental database using MySQL or PostgreSQL is one example. You won't have to worry about counting users and renewing subscriptions. Instead of budgeting money, you'll be budgeting personnel hours to the project.
It's free software only if your time is free, but a good analogy is replacing a faucet at home:
a.) Are your skills up to the job at hand?
b.) Do you want to pick out the very faucet you want at the price you want, or are you willing to settle for what the plumber brings?
c.) Considering your time vs. the plumber's bill, is it worth it to you to call him or to do it yourself?
And the icing on the cake is that you do get better with each project.
Dig deeper on Enterprise applications for Linux
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