I can answer only a few questions, but running linux nearly exclusive, I like to welcome you.
to 1)
I favor Postgres over MySql.
- When I started with linux in the mid-90's, MySql looked poor.
- I didn't and don't like the name.
- Postgresql's frontend looked much like Oracle5/sqlPlus where I learned sql on Dos (no joke
.
- Whenever I read a comparision of postgres/mysql, postgresql was much more advanced, closer to sql-standards and as far as I know it is still. There are no views and no subqueries in MySql as far as I'm informed.
- I don't like webapps, and mySql is intensively used in webapps
- Postgres looks professional, mySql looks like a clown.
If you go for WebApps MySql might be a better choice - if you like to be close to standards, postgres is the better choice.
related:
to 6) As far as I know, JDO is available in dependence of the vendor, for example available for oracle, not for postgres - but I'm not sure about that - better you wait for a better answer.
to 7) It is the de-facto standard, but often people use jdbc-odbc, due to old (and I mean: really old) tutorials, books, habits. I can't proove it is slow, but often people use it in a slow way/ bad habit - combined with a lack of sql-knowledge, missing indexes and so on, you can make it really slow. I didn't see a comparision/ performance-test till now.
to 5) What do you mean with 'open source implementation'?
The gnu compiler has a gcj - java compiler but I don't know why to use it, since I don't intend to extend it
.
The classes (API, jars) for linux are released at same time to linux as to windows. The jre may be distributed (to run your programs). You're free to distribute the j2sdk-classes (don't know about j2ee) so I don't see a real need for OpenSource release.
The API-source is open in that way, that you may look at it (src.zip) which is very useful for debugging and in the rare-case you search for a bug.
It is not open in the way the Open - Source - Community talks about it: changeable, redistributable.
There was/(is?) a (FSF?)-project blackdown.org but I didn't visit it for a longer time.
There is a freely available compiler 'jikes' from ibm too, which has been faster in former times - but again I'm not up to date.
Being not a dogmatic OpenSource - hacker, I don't see much benefit in searching for a non-sun-java. Of course this could change in the future, but as John M. Keynes told: in the long range we all are dead.
If you visit blackdown, see how far they are on the upcoming standard of j1.5 - I guess beeing up to date was the most important point for me sticking to sun.
to 8) The fat-GUI is much enhanced by the swing-projekt, which isn't that new any more
. Eclipse uses it's own GUI-LIB: SWT, which is told to bring more beauty on the desktop. Well - I like eclipse, but don't spend much observance on GUI - Look-and-Feel - not enough to learn one more API.
to Number Nine) I'm sorry, being unable to give you a good hint.
To an experienced programmer, coming from a language which was inspired by java and being comfortable with design-patterns etc., I guess you will need two things: Experience with the API, and the pitfalls of starting a java-app, generating a jar and so on.
A 'Java-core' book from sun was quite well for me, and 'O'Reilly: Examples in a nutshell'.
Hope you soon feel comfortable with java on linux