Yes. First you need a homebrew-capable flash cart, writable medium for that cart, and the actual voip program.
My personal choice is to use a slot-2 (GBA) flash cart, such as the SupercardSD, M3 (slot 2.. not sure of the name), or CycloDS-SD. You could get a Slot-1, but since they don't include the RAM extension that SvSIP and many other fun programs recommend, it's not really worth it. My setup is a CycloDS-SD, running Supercard firmware v. 1.6, with flashed firmware on my DS itself.
For VOIP, my fav. program is SvSIP, which allows dialing out and receiving calls while the program is running. You do, however, need an account through a VOIP provider (the free acct for FreeCall will work just fine for this). Another possibility is VoiceChatClient, which is more like a DS-to-DS chat client, but it still functions.