I currently run business courses where I print my own certificates.  I
would like to increase the security / professional look of my
certificates by including a customized watermark similar to the type
of watermarks found on bank notes (where you can hold the certificate
up to the light and see a watermark).  I stress this must be my own
customized watermark and not pre bought blank certificates.   In
addition it would be helpful if I could include similar security
measures like embedded foil strip / hologram / etc.

Am I likely to need specialist equipment for making my certificates
and if so what equipment should I purchase and are there any internet
guides detailing such procedures?

I have been doing some research for a new business of my own.... 
Check out the webpage link below.  I think that you will find it may
provide some answers to what you are looking for.  Good Luck!

http://www.novavisioninc.com/pages/prd_hologram_labels.html

Watermarks are created in the paper-making process.  That is what
makes them a security feature, just like imbeded foil strips and
holograms.  All three are security feathers in Euro banknotes, because
they are very difficult (not cheap) to duplicate.
I think that there are printing methods to approximate a water mark.

For your certificates, I would suggest that they are consecultively
numbered and "fancil<" enough printed to discourage copying.

As mentioned - Watermarking and Foil strips etc are all part of the
paper manufacturing process and unless you plan to make your own paper
(which is not impossible ) or know someone else who does, these are
not viable options.
I would suggest a slightly different approach - have an embossed die
made to imprint an embossed mark on the page. It is as permanent as
the paper. Once the cost of the die is met there is no further
'running costs'. It is difficult to copy (even for good forgers). And
it will add a certain 'je ne sais quoi' to your certificates.
Failing that - what about a wax seal?

Thank you all very much for your comments, kidscook stated that
Watermarking and Foil strips etc are all part of the paper
manufacturing process and cannot be used unless I plan making my own
paper (which is not impossible).  Out of interest if I planned to go
this route, are there any internet guides / books detailing how I
would do this?