I've added and updated the journals section of the sidebar. For the most part, I am including just those that have significant Civil War content and have useful online content free of charge (ex. table of contents, search capability, full articles, etc.). Civil War History has a notably poor free online presence, but hopefully they'll see fit someday to at least include some kind of minimal citation info on their site. Some of the others do have TOCs but neglect the page numbers, which would be more than slightly helpful in obtaining copies of the articles through interlibrary loan. Please feel free to offer journal suggestions of your own in the comments section.
If I recall correctly from my quick breeze through them all earlier in the week, only the Kansas, Oklahoma, Ohio, and Florida state historical society journals provide many or a majority of their articles from their run for free online. Florida HQ offers complete content on seemingly all of their volumes, but I've found the search capability to be very frustrating. As an update, the Register of the Kentucky HS now has a pdf file containing the table of contents for all of its issues for viewing or download.
[Addendum: MUSE does have TOC info for CWH available for Vol. 46, no. 4 (2000) through current issue. A subscription is needed for access to the content.]