Posted 07 May 2012 - 10:50 AM
Most of the answers to your questions are going to vary from one directory to another, and you should look for their requirements before you submit your information, but I'll try to give you some information here.
1. Odds are if they're asking for keywords to be separated by commas, they mean you should enter keyword phrases separated by commas, e.g. "search engine optimization, search engine marketing, internet marketing"
2. Their rules regarding site description will vary a lot, but they should indicate on the form how many characters you're permitted to enter. For the actual content of the description, a lot of directories are going to insist on a very straightforward description of what the site is about and what it has to offer. If you want to consider the ODP (dmoz.org) as a standard, they don't want you to enter any comparative or superlative terms (no "best site for" or "offers large selection").
3. Deep links are URLs for pages other than your site's home page. Some directories have an absolute rule stating that the only URL you can enter is the site's default page. Others will allow you to list a number of internal pages, usually for an additional submission fee.
4. A lot of directories that will let you put something like keywords into your listing's title are kind of spammy -- they often refer to themselves as "SEO friendly," meaning they let you get away with a lot. The more reliable directories -- the ones search engines are probably more likely to care about -- will usually require you to put your company's name and nothing else into the title.
5. Yes, this is related to #4. On the more respectable directories, you're not going to have the opportunity to put the contents of your home page's title tag anywhere, unless your home page's title tag happens to be nothing more than your company name.