I recently released the R package crossmeta on Bioconductor which streamlines the cross-platform and cross-species meta-analysis of microarray data. All you need is a list of GSEs for which you would like to perform a meta-analysis.
crossmeta automates downloading, pre-processing, annotating, and batch variable correction of raw data from GEO. You can check out the vignette for usage details. I also have a couple of posts on my blog that evaluate
crossmeta and demonstrate the type of analysis that is possible.