I wrote a CMS using php and MySQL for a hockey team. I have built this up over 4-5 years.
The CMS allows the client to input:
players
rosters
schedule/results
news
banner adds
video links
photo links
blog section
moments in history
player records
free format web page
navigation
upload pics, banners, graphics
etc.
We have traded services for payment. My services. Their season tickets, league pass to all games, clothing, laptop, etc.
Now I have another team interested in my work and they want a price. I don’t have an idea what to charge for the scripting I have done.
I would plan to load my scripts to their host give them some training and let them have at it.
My question are:
What to charge for my app
How to protect my app from being used else where for free
I am sure I will have to do some general maintence through the year so what type of flat rate to charge them
If the keep it would I charge them some type of annual maintenance fee
What else have I left out? I don’t know what I don’t know. 
Congrats on your success there - it feels good to be wanted don’t it? 
You’ve got some good questions there and unfortunately all I have for you right now are more questions - like…
Are the other products like yours a team could use to manage their site? If so, what to they cost?
If not, what value would you place on the site you’ve developed? Sounds like you’ve gotten some great free perks in trade - can you put a dollar value on those items? How many hours would you say you invested in this, and what would that work out to if you charged the average hourly rate of a web developer?
I don’t think anyone could give you an exact answer here, but if you can come up with a ballpark figure to start with, I’d probably say double it and then see what they say. Be prepared to show them the value of what you’re offering and how much time and money they’ll save in the long rin by hiring you. The worst they can do is say “no” and make a counter offer - which you can consider and decide what works best for you both.
Of course you can always try asking upfront “what would you pay for something like this” - but chances are you’ll get a low ball number and you you’ll end up settling on a lower number than if you had started higher and worked your way down.
Cheers,
Steve
P.S. Welcome to Sitepoint too, and if this is something a second team is interested in now, consider how many other teams might find it helpful and think of ways you could package this to sell to multiple teams. 