The TruSeq DNA/RNA, old PE (Paired-End) Genomic DNA, Nextera, and old Paired-End Multiplexing adapters work on all Illumina platforms and can be read as a single read or paired read.
TruSeq small RNA adapters will work on all platforms, but can only be used for a single forward read.
The OLD small RNA adapters work only for a forward read on Single Read flowcells on the HiSeq2000 or GA, and we strongly recommend you do not use them to build new libraries.
IF YOU USE THE ILLUMINA ADAPTERS WITH THE INTERNAL INDEXES, AND YOU WANT THOSE READ, YOU MUST ORDER A MULTIPLEX READ when you submit your sample. This is an extra priming and sequencing read and will cost extra.
See the FAQ about indexes vs barcodes if you are interested in doing the barcoding "inline" within the main fragment read.