A characteristic of each of the existing second generation sequencing instruments is that each manufacturer provides its own collection of sample preparation reagents and kits.
Some of this variation is inherent to a particular platform. For example, the use of terminal transferase tailing is part of the supposed charm of the Helicos sample prep. Polonator needs to use a series of tag generation steps to overcome its extremely short read length. Illumina's flowcells need to be doped with specific oligos. So, some of this is natural.
On the other hand, it does complicate matters -- especially for various third parties which are producing sample preparation options. For example, targeted resequencing using hybridization really needs to have the sequencing adapters blocked with competing oligos -- and those will depend on which platform the sample has been prepared for. Epicentre has a clever technology using engineered transposases to hop amplification tags into template molecules -- but this must be adapted for each platform. Various academic protocols are developed with one platform in mind, even when there is really no striking functional reason for platform-specificity -- but a protocol developed on one really needs to be recalibrated for any other. And in any case, it would great for benchmarking instruments if precisely the same library could be fed into multiple machines -- and it would be great for researchers looking to buy sequencing capacity on the open market to be able to defer committing to a platform to the last minute.
In light of all this, it is interesting to contemplate whether this trend will continue. One semi-counter trend has been for all three major players, 454, Illumina and SOLiD, to announce smaller versions of their top instruments. Not only will these require less up-front investment, but they will apparently use all the same consumables as their big siblings -- but not as efficiently. So if you are looking at cost per base in reagents, they won't look good.
However, an even more interesting trend that might emerge is for new players to piggy-back atop the old. Ion Torrent has dropped a hint that they might pursue this direction -- while the precise sample preparation process has yet to be announced (and the ultimate stages prior to loading on the sequencer are likely to be platform-specific), Jonathon Rothberg suggested in his Marco Island talk (according to reports) that the instrument could sequence any library currently in existence. This suggests that they may be willing to encourage & support preparing libraries with other platform's kits.
Of course, for the green eyeshade folks at the companies this is a big trade-off. On the one hand, it means a new entrant can leverage all the existing preparation products and experience. Furthermore, it means a new instrument could easily enter an existing workflow. The Ion Torrent machine is particularly intriguing here as a potential QC check on a library prior to running on a big machine -- at $500 a run (proposed) it would be worth it (particularly if playing with method development) and with a very short runtime it wouldn't add much to the overall time for sequencing. PacBio may play in this space also, if libraries can be easily popped in. This also acts as a "camel's nose in the tent" strategy for gaining adoption -- first come in as a QC & backstop, later munch up the whole process.
Of course the other side of the equation for the money counters is that selling kits is potentially lucrative. Indeed, it could be so lucrative that an overt attempt to leverage other folks kits might meet with nasty (and silly) legal strategies -- such as a kit being licensed only for use with a particular platform. That would be silly -- if you are making money off every kit, why not market to all comers?