The Washington Post's God in Government blog argues Justice Souter's replacement could "alter the church-state mix" on the court. Indeed, it's hard to see how President Obama will find a nominee with Souter's blend of passionate support for both a strong Establishment Clause and a strong Free Exercise Clause.
Souter is known for voting for and writing for a strict separation of church and state, which for him meant rejecting any taxpayer money for the direct support of religion, including vouchers for religious schools, for example. Interestingly, he also argued strongly that the First Amendment's free exercise clause should be understood to exempt religious practices from laws that burden those practices – even if the government didn't intend to suppress religion.
In other words, he was known for robustly arguing for church-state separation, but also strong support for individual religious freedom.
The post quotes some detractors who feel Souter goes too far in endorsing the "strictest separation of church and state". Whether or not he was always right in his opinion the voice of separation is a perspective that needs to be heard, in my opinion. Do they even make judges with Souter's point of view on this issue any more? The Court's collective voice on church-state matters seems sure to change, even if just in the loss of a compelling dissent.
Browse Religion Clause's list of Souter's church-state opinions here.