Merging sequencing data for ChIP-seq experiments I need to merge sequencing data from different sequencing runs but for the same ChiP-seq library (HiSeq 2000).

Are there any potential advantages or disadvantages when merging files at .fastq or .BAM stage (alignment with Bowite/1.1.2)?
I don’t think it matters. Both are easy to merge (BAM via samtools merge, and (gzipped) FASTQ via cat), and neither method has specific disadvantages, unless your FASTQ files are sorted for some reason (but they generally shouldn’t be).

One advantage of keeping the FASTQ files separate is that it makes it slightly easier to parallelise the mapping step: just run the mapper in parallel on the separate FASTQ files. Although bowtie has an option (-p) for this, throughput from that is slightly worse than running the mapping on split files.