Well, that's just asking for a massive open ended debate.
Personally, i would say if you have a bespoke system that does what you want and satisfies any statutory reporting needs, then stick with it. You will only find that any off the shelf product is going to be painful to use and not always do what you want. Changing MIS is such a huge task that any problems will have staff begging to go back to the old system.
Nonetheless, it's useful to go and see what other schools are doing. SIMS has many partnership schools, and i'm sure Serco,Bromcom,Integris and the others all do too. It would be best to see what they do for real and compare to your own solutions.
To answer your points in brief:
1) I don't know of (m)any schools that use bespoke MIS Systems, maybe colleges or independent institutions. Many places use an off-the-shelf product and have advanced methods to rip data out and customise it via access dbs, scripts, web pages etc.
2) I wouldn't say that the standard MIS systems are customisable, they tend to be standard fits that on the whole work for most schools. However, they should cover all the points you require. I can speak for SIMS:
a) Medical data is stored and can be accessed from register but doesn't display by default, though there are no systems that link in to the register that collate this info either via sharepoint webparts or other software.3) Access to database is not permitted but some people have virtual cloned setups where they can read the SQL. The schema is not published as far as i know and is far from easy, though some of us do use it for access. You should be able to offer info from the db via webparts in sharepoint. There is a command reporter tool that allows you to schedule and run predefined reports, as well as a pretty extensive reporting module. I think this is an area you will find all box product MISes lacking though.
b) There is an advanced reporting system, soon to be radically altered and improved upon. Results can be exported to word/excel etc and/or published to sharepoint.
c) There is an add-on module to SIMS called FMS that handles finances from purchasing to billing of parents to salary. It's pretty robust and can live on the same SQL server.
d) There are tutor groups and house groups and a separate reporting module called Profiles. Report writing tasks including checking and reviewing are available and setup through the timetable / pastoral structure. Short reports can also be done via the assessment module.
e) Traffic lighting is possible, it just needs some setting up in the assessment module. I think there is a summary view where behaviour is automatically color coded. Attendance has a default traffic lighting option in this view.
f) There is a behaviour / achievement module which is very useful but can be a bit clunky. I'm not sure how you'd get your form onto the system, it would depend on what data goes onto it. You can earn positive / negative points and these could be linked to house points...
4) I think all systems now offer parental access of sorts because of the DCSF requirements. This is done via webparts into sharepoint. SIMS supply their own, or many other companies have their own more tailored versions. There are also other products from licenced partners that can tap in and extract the data for presentation as well as allow read/write access.
5) All schools now really should have at least 1 dedicated member of staff responsible for day to day running of the system. In addition, there are often other key members of staff that take on responsibility for specific areas e.g. timetabling, personnel, absence, reporting etc. More and more there are bespoke MIS people in secondaries but often it falls on to the desk of the IT manager / technician to handle the MIS. It's primaries that suffer the most.
I hope that's of help. Any more questions, feel free to ask.
Have a search of the MIS forum, there have been many recent threads regarding which MIS to use and the relative benefits. Don't be disheartened by the griping, everyone likes to have a good whinge about their MIS from time to time.