There are two principal differences between the WELS and the LCMS. The first is their respective understandings of church fellowship. The WELS has a ‘unit’ concept of fellowship; they believe that all aspects of fellowship are on the same level. This means that altar fellowship is placed on the same level as prayer fellowship. As such, WELS are very careful about prayer and will generally not pray publicly with those who are not in communion with their Synod. The LCMS has historically distinguished between types of fellowship; i.e. an LCMS pastor will not (or should not anyway) commune someone who is not LCMS or one of her sister churches abroad. However, an LCMS pastor may pray with Christians of other denominations.
The second large difference is regarding the office of the holy ministry. The LCMS teaches that the pastoral office is distinctly ordained by Christ, and therefore should be thought of in a different light than other functions of the ministry (i.e. teachers and elders, etc.) The LCMS sees these different offices as being created by man for the benefit of the church and to fulfill her purpose, whereas the WELS Theses on Church and Ministry states that the pastoral office is not instituted apart from the other offices of the church.
One other difference is that women can vote on congregational matters in most LCMS congregations (an LCMS congregation’s constitution, rather than the Synod, determines this for each congregation) whereas women are not permitted to vote in the Wisconsin Synod.
It should be noted, though that the WELS and LCMS agree 99% of the time. Specifically with the current questions of female ordination and homosexual marriage/ordination, the LCMS and WELS have been in lock-step together. They have the same understanding of the role and nature of Holy Scripture and the Lutheran Confessions in the life of the church.
I pray daily for our misguided brothers in the ELCA. To be honest, the most liberal 1% of the ELCA happens to be the 1% guiding the direction of the church. At my home LCMS congregation, we have received about 100 phone calls over the past few weeks from scared ELCA members who want to learn about conversion to the LCMS. There are many more conservative church members in the ELCA than the public perceives. The problem is that the ELCA gives their congregations too much autonomy.
I believe that there will soon be another split. I hope that the conservative faction of the ELCA will merge into either the LCMS or WELS, rather than creating a new church body (which is the last thing we need.)