I spent several hours cleaning up my contact list on my iPhone 3GS. Will they either be deleted, or added to by my previously backed up list on itunes, when I re-connect to itunes?
Syncing will overwrite your previous backup, it will not transfer anything from the backup to your phone (unless you are restoring from backup). However, the backup only maintains contacts to preserve your favorites and recently called list. This is from Apple:
"Your contacts are part of the backup to preserve recent calls and favorites lists. Back up your contacts to a supported personal information manager (PIM), iCloud, or another cloud-based service to avoid any potential contact data loss." (Reference http://support.apple.com/kb/HT4946).
You should not rely on the backup to archive your contacts; there have been many cases when they were not preserved and users lost their contacts when restoring from a backup. If you can't sync with Outlook or a supported program for contacts then you should sync them with a cloud service (iCloud, Google, Yahoo, etc.) so they are safe.