Using /var/www for my web root, I create /var/www/sites and symlink my sites directory to it, and /var/www/files for robots.txt. It makes upgrading (in the absence of an SCM) less scary, just overwrite the /var/www/drupal folder with the new version and hit update.php.
Use a local copy of drupal for your development; it's much less of a pain to debug locally than over the WAN, and easier for you to use your site's code as a project in your IDE, which (may or may not, dep. on your IDE) provide you with code completion and easy access to your files. When you're done you can push the changes via ftp/scp, or using whatever SCM you are familiar with.
I use devel's dsm() function liberally, so i would recommend that module. It makes debugging-without-a-debugger (i.e. after prod. move) much less painful.
Also, Admin Menu makes administering your site much easier; it gives you dhtml popup menu access to all the admin pages, in a hierarchy, so there's only one click between you and most admin functions.