Firstly, be aware that System Center is a product suite rather then a product. I think what you are referring to is System Center Operations Manager 2007 agents.
In which case, firstly you'll most likely want to be using Operations Manager 2007 R2 which is the newest version, its quite a bit more 'polished' then the original version of Ops manager 2007 which had the Linux/Unix monitoring kinda wedged in there. R2 is publicly available from July 1st, but you can grab an Eval copy now.
Because R2 is kinda new, there's not too many people using it yet in production, but certainly people have been testing and blogging about it on the beta and release candidates. Google 'operations manager 2007 Linux' should give you some hits.
There is a quick datasheet PDF on the R2 Linux monitoring component available.
A good start for monitoring Linux/Unix would be to check out the Microsoft webcast, or to read the R2 install docs for the Unix/Linux agents on Technet.
Also definitely keep an eye out on the Technet Forums.
Once you're up and running you could look at third party management packs for monitoring Apache, MySQL etc from companies such as Bridgeways.