What is the best value way to travel by rail from Southend airport to ExCel in London and then to Gatwick?

Before continuing, you should probably read up on the different kinds of tickets offered on the UK rail network. This looks to be a fairly comprehensive list. The things you'll especially want to take note of are the general kinds of times they apply to, and the rules around Break Of Journey (which affect if you can stop and continue, eg to go to your conference)

For a journey like that, there are basically three options, which you'll need to price up. Firstly, Southend Airport to Gatwick single, coupled with another ticket or Oyster Card for when you break your journey and go off-route to get to/from the ExCel. Secondly, Southend Airport to ExCel (Custom House), then ExCel to Gatwick. Finally, one airport to the edge of London as a single, the other with a London Travelcard all zones (eg Southend -> Stratford anytime single, plus Gatwick to London off-peak day Travelcard 1-6 return). Options #1 and #3 would allow you to stop off to, say, do a tiny bit of sightseeing, get some dinner etc.

Without knowing your exact journey times, and what railcards you may have, we can't tell you which will be the cheapest. What you should do is use something like the National Rail Enquiries Journey Planner to tell you times+prices for the different options, along with the TFL TravelCard pages + TFL Fares page to work out the cost of going off-route if you bought a Southend Airport -> Gatwick station and broke your journey.

My hunch is that #2 will be cheapest for an early morning, #1 for shoulder peak, and #3 for off-peak, but you will need to try the combinations for your chosen times to see.

One possibly good thing for you - none of the routes in question seem to offer advanced purchase fares, so there's no advantage (other than time) for buying in advance