In regards to single end SOLiD sequences (50bp) for the purpose of ChIP-seq:

Corona-Lite

I used to always use this as i thought the uniquely mapped reads was the safest option. Plus it gave a good %mapping rate compared other mappers i played with. The disadvantage is that it does not produce native SAM output and the conversion process is lengthy and the product is not compatible with downstream tools. It is also no longer being developed and has been replace by Bioscope, which i believe is now being replaced by Lifescope.

BFAST

I made the decision to move over to BFAST as i was impressed by what i heard about it from conferences etc. The indexes are BIG and slow to create though. The main reason i like it is because of the 'postprocess' flag '-a3' that returns uniquely mapping reads and reads that map to multiple locations, but where one match scores better than the rest. It also does not appear (to me) to constrain the output reads by the number of mismatches, but this is tricky as read matches may contain INDELS (see below).

As i side note it is good for resequencing projects as it is a 'gapped aligner', which means it will find matches to reads containing INDELS.

LIMBO

I am currently in a state of limbo as some users/customers of our facility like the output of Corona-Lite compared to BFAST and visa versa. One scenario of note is when matching reads to repeat regions. BFAST produces some very large peaks in these areas compared to Corona-Lite; it is not clear at the moment which program is 'telling the truth'.

PerM I like a lot of PerM functionality, but it does throw away all reads that contain color miscalls (-1). I played with this tool just after it was released and has come on leaps and bounds. I probably should retry it...

I only have experience with Illumina reads. So, BWA, novoalign for genomic DNA reads, variant calling, I also used a bowtie/novoalign two-step mapping for genomic DNA reads and it worked very well; Bowtie (PE or SE) for mRNA-Seq expression analyses. I'd like to mention BLAT, although it's not really a mapper. BLAT is very good for evaluating contigs from de novo assembly of mRNA-Seq reads, very fast, accurate and the results are easy to parse.

You might be interested in this recent paper:

"Comparative analysis of algorithms for next-generation sequencing read alignment"

http://bioinformatics.oxfordjournals.org/content/early/2011/08/19/bioinformatics.btr477

Tophat for RNA-seq data. BWA for genomic.

More of your experience are stil welcome.

Thank you