One application of pseudo 2-limits (bilimits) in algebraic geometry is already found in the definition itself of stacks with values in a 2-category admitting bilimits (i.e. a discrete 1-cell-contravariant pseudo functor defined on a site). Of course there is the general notion of descent, etc. and all of its applications. There are also 2-colimit generalisations of aspects of Grothendieck's Galois theory (from SGA1) and aspects of SGA2.
The question is then whether there are "interesting" situations (not necessarily from algebraic geometry) where one must use lax 2-limits and cannot get away with just using pseudo 2-limits? (Or 2-colimits?)