i have exactly the same problem. i'm not sure when it started and i did not upgrade everytime a new version came out. i am, however, pretty sure that it began with or after 2.0. i remember that i got a "500 Internal Error" occasionally while posting a new entry, so i updated to the next version of WP and it seemed to be fixed...for now. but after a while i noticed that it took longer and longer to open the "write" page and to edit entries. last summer it took 20 seconds, but these days i have to wait around 1-2 minutes, whichmakes me think that the problem is increasing while the database becomes bigger. just for the record: my DB has about 35MB and consists of roughly 700 entries, which is not *that* huge.
at first i started to blame my host, but then i started playing around with a local webserver (xampp). i did two instllations, one on my laptop and one on my desktop pc:
1) xampp with a new, clean WP 2.1.2. installation.
2) xampp with WP 2.1.2. installation AND my old database.
now guess what. the sql/apache settings are the same on both, and while the new installation works like charm, the one with my old database shows EXACTLY the same symptoms as mentioned above.
i did a bit of research, and this is what i found out: whenever i try to open the "write new entry" page or try to edit an older entry, my HD space decreases by 300-400 MB and the CPU usage goes up by 10-15% (due to the server writing a .temp file - but why?)
in the phpmyadmin panel, the following process appears to be the problem:
Status: Sorting for group
GROUP BY meta_key
ORDER BY meta_id DESC
sometimes the text edit window appears, incl. the modules on the right side, but the page still takes another 2-3 minutes to build the upload/trackback/user defined modules.
i'm not an sql expert and i don't know how i can optimize the database, but i guess that it's the database itself that is causing the problem, since the symptoms on two different servers are the same, while a new WP installation works perfectly.
if anyone has an idea, please let me know.
[and yes, i tried all the mentioned fixes - plugins, pingbacks etc..]