Firstly, I presume that each panel member is employed by one company only- each one employed by a different company.

We now use 'their' in place of his/her, but we still mean 'each individual panel member will discuss his/her general use of applications'.

Political Correctness propels us into the uncertainty you are facing.

Since each individual panel member is contributing his/her perspective from his/her experience within his/her company, the best rendition is (1):

Panel participants will discuss their company’s general use of the various applications.

(Note: it cannot be (2), because of where we place the apostrophe with singular versus plural nouns. Let me know - we could cover that too.)