The stoppers on the 96-Present DR650SE are not too bad actually, and definitely better than the brakes on its nearest competitor, the KLR650. But there is always room for improvement such as stickier pads or a set of stainless steel brake lines. The stock rubber brake lines expand when braking and slightly reduce the braking effect, so stainless steel brake lines can be effective. There is a lot of debate about whether wave discs have any benefit or not, but there are cheap Chinese made ones if you want to explore that option.
EBC now make a 320mm floating front disc with caliper adapter that is available as cheaply as $210 and should give slightly better braking performance.