I'm upgrading from MT 3.33 to MT 4.21. On 3.33 I'm running a few plugins that will have their own upgrade routines, MT Blogroll -> Linkroller, MT Notifier, Photogallery, Rightfields -> Custom Fields, etc. I'm also doing a clean install upgrade.
The upgrade instructions I've seen seem to suggest uploading MT 4.2 and all the new plugins and then hitting mt.cgi. Something tells me that if MT tries to upgrade and all those plugins do too, I'm going to have issues. On the other hand, my templates and database all rely on those plugins being there.
So what is the best way to proceed, upload the plugins before the upgrade to 4.21 or upgrade MT and then do the plugins one at a time?
Reported on Movable Type 4.2

The latter, probably. Just doing the database upgrades for Movable Type shouldn't run into any issues at all when you hit mt.cgi; rebuilds should be the only thing affected in the mean time, which you're probably prepared for right now anyway. What I'd recommend is:
1) Export your blog AND do a database backup so you have copies of most of your important data in both forms to give you options later.
2) If you can, log into your host via SSH or Telnet and run "zip -r mt.zip MOVABLE_TYPE_DIRECTORY" to create a backup zip file of your existing MT installation.
3) Install a fresh, new copy of Movable Type 4.21 and set up mt-config.cgi.
4) Run mt.cgi to upgrade your core database tables.
5) Manually install all of the plugins.