We have done both, we have found greater flexibility with salary when it comes to negotiating a package.
Perks we have previously negotiated are extra holiday time, car allowances, RDOs, phones, bonuses ect
Salary is good for budgeting, you know what money your receiving and you not getting a cent more! Sometimes it works out quite well, work is a bit slow not alot on and the pay is good for the hours worked but mostly it has been lots of work, lots of pressure and lots of hours and no home life for what works out to be a pretty dismal hourly rate.
We have found that working in a larger company on salary is ok because there is usually more than one of you and you can be backed up and helped out, you just have to deal with the red tape that at times almost makes it impossible to do your job. In a small company where there is no one else to help spread the load then you end up doing long hours.