I've started to make SEO for our Web Design Company Cratima
and one of the problems I am confronting with is that there is
a fee difference between different web directories on the web.

I can submit our site to free web directories, reciprocal link directories,
and paid directories.

Now, my question is: is there really a difference between this submissions?
I mean, does Google index your site depending on the amount of money you pay a web directory site? Or do this paid web directories offer services that help Google index your site better?

I'm looking forward for your replies, thanks !

First of all, do NOT submit your site to reciprocal link directories. This will boost your ranking in the short term, but in the long run, it will kill you. Link spam is on the verge of being blacklisted by Google (and we all know that is the only search engine that matters anymore). I'm not saying to not exchange links, but if you do, make sure it is a site with actual contect, and not just a bunch of useless junk on there.

Secondly, you don't have to pay to be in a directory. Anyone who says you do is full of it. Google indexes your site the same, regardless of if you spend $1000 on a submission or nothing. The best way to optomize your site is the same old fashioned way. Keep your spiders.txt file up to date, and make sure your site is fairly W3C compliant. The spiders will find their way through a lot easier and your rankings will increase because of it.

Yes,
I've just heard that Google banns all the web sites that use paid directories.
A colleague of mine at Cratima Interactive has just sent yesterday an
e-mail to Google to ask for more details, no answer yet.
Thanks for your message.