My favorite source for malicious samples is a database i assembled myself by regulary pulling the free examples provided by VirusSign. Please not these samples do require registration, but come with reports indicating the type.
There may be no better archive for malicious samples than VirusTotal. If you don't happen to gain (intelligence) access there, you can still try open alternatives like Open Malware.
Generally, a good list for places to find malicious samples is here:
As for benign samples, I propose extracting benign executables from a fresh OS installations. You can simply install the target in a virtual machine and get a script to extract them.
Another source is crawling sites like PortableFreeware. Please make sure you check if executables collected this way to work in your environment.
Possible false positives
Most malware archives label their samples based on the detection ratio and labels provided by different ant-malware products (like VirusTotal). Asssuming samples with very low detection ratio and generic labels to be false positives is probably the best way to go here. Also, data collected from HoneyPots may yield relatively higher false positive rates.
I often used the executables included in the Sysinternals Suite as a kind of 'false positives'. They are benign binaries utilizing system-near features in order to expose system internal data.
On a sitenode, please take time evaluating your dataset and finding biases hidden within. A lot of current research suffers from biased sample sets and unreproducible results.