Transitioning to lead-free reflow and soldering
The challenges with lead free are these:


A higher melting point 
Higher thermal EMF  
Maybe less re-workability


With a higher melting point this can create problems, especially during rework. This can create problems for components, and for prototyping as that involves reworking and replacing parts. It can also create problems for mechanical components or components with large footprints or heatsinks as the temperature must be even higher than before. 


Source: http://www.aimsolder.com/alloys

The other problem is a higher thermal EMF, which is the offset produced by the seebeck effect and usually in the uV. This can be noticeable if your working with signals on a uV level and gaining them up with analog electronics. 

Another thing to keep in mind is switching solders can also mean switching fluxes and that can create problems. Read up on the flux or sample solder before buying to see if it will meet your needs. The flux can also contribute to how easy it is to rework the solder.

For me personally I'm a fan of SAC405, it's not what most of the assembly houses use so if your trying to match solders, that won't work because most use SAC305.

I got these from qualitek and I a pretty happy with them and the price. One is water soluble and one is no clean (can't remember which). 
DSP SAC405 - Type 863 or DSP SAC405 Type 798LF