Web-based multi-AV scanners, and malware sandboxes for automated analysis.

https://sandbox.anlyz.io/]anlyz.io

 - Online sandbox.

https://app.any.run/]any.run

 - Online interactive sandbox.

https://andrototal.org/]AndroTotal

 - Free online analysis of APKs against multiple mobile antivirus apps.

https://avcaesar.malware.lu/]AVCaesar

 - Malware.lu online scanner and malware repository.

http://www.cryptam.com/]Cryptam

 - Analyze suspicious office documents.

https://cuckoosandbox.org/]Cuckoo Sandbox

 - Open source, self hosted sandbox and automated analysis system.

https://github.com/brad-accuvant/cuckoo-modified]cuckoo-modified

 - Modified version of Cuckoo Sandbox released under the GPL. Not merged upstream due to legal concerns by the author.

https://github.com/keithjjones/cuckoo-modified-api]cuckoo-modified-api

 - A Python API used to control a cuckoo-modified sandbox.

https://www.deepviz.com/]DeepViz

 - Multi-format file analyzer with machine-learning classification.

https://github.com/detuxsandbox/detux/]detux

 - A sandbox developed to do traffic analysis of Linux malwares and capturing IOCs.

https://github.com/tklengyel/drakvuf]DRAKVUF

 - Dynamic malware analysis system.

http://firmware.re/]firmware.re

 - Unpacks, scans and analyzes almost any firmware package.

https://github.com/Tencent/HaboMalHunter]HaboMalHunter

 - An Automated Malware Analysis Tool for Linux ELF Files.

https://www.hybrid-analysis.com/]Hybrid Analysis

 - Online malware analysis tool, powered by VxSandbox.

https://analyze.intezer.com/]Intezer

 - Detect, analyze, and categorize malware by identifying code reuse and code similarities.

http://irma.quarkslab.com/]IRMA

 - An asynchronous and customizable analysis platform for suspicious files.

https://www.joesecurity.org/]Joe Sandbox

 - Deep malware analysis with Joe Sandbox.

https://virusscan.jotti.org/en]Jotti

 - Free online multi-AV scanner.

https://github.com/monnappa22/Limon]Limon

 - Sandbox for Analyzing Linux Malware.

https://github.com/rieck/malheur]Malheur

 - Automatic sandboxed analysis of malware behavior.

https://github.com/maliceio/malice]malice.io

 - Massively scalable malware analysis framework.

https://github.com/diogo-fernan/malsub]malsub

 - A Python RESTful API framework for online malware and URL analysis services.

https://malwareconfig.com/]Malware config

 - Extract, decode and display online the configuration settings from common malwares.

https://malwr.com/]Malwr

 - Free analysis with an online Cuckoo Sandbox instance.

https://metadefender.opswat.com/]MetaDefender Cloud

 - Scan a file, hash, IP, URL or domain address for malware for free.

https://www.networktotal.com/index.html]NetworkTotal

 - A service that analyzes pcap files and facilitates the quick detection of viruses, worms, trojans, and all kinds of malware using Suricata configured with EmergingThreats Pro.

https://github.com/Rurik/Noriben]Noriben

 - Uses Sysinternals Procmon to collect information about malware in a sandboxed environment.

https://packettotal.com/]PacketTotal

 - PacketTotal is an online engine for analyzing .pcap files, and visualizing the network traffic within.

http://www.pdfexaminer.com/]PDF Examiner

 - Analyse suspicious PDF files.

http://www.procdot.com/]ProcDot

 - A graphical malware analysis tool kit.

https://github.com/secretsquirrel/recomposer]Recomposer

 - A helper script for safely uploading binaries to sandbox sites.

https://github.com/InQuest/python-sandboxapi]sandboxapi

 - Python library for building integrations with several open source and commercial malware sandboxes.

https://github.com/F-Secure/see]SEE

 - Sandboxed Execution Environment (SEE) is a framework for building test automation in secured Environments.

https://malware.sekoia.fr/]SEKOIA Dropper Analysis

 - Online dropper analysis (Js, VBScript, Microsoft Office, PDF).

https://www.virustotal.com/]VirusTotal

 - Free online analysis of malware samples and URLs

https://github.com/keithjjones/visualize_logs]Visualize_Logs

 - Open source visualization library and command line tools for logs. (Cuckoo, Procmon, more to come...)

https://zeltser.com/automated-malware-analysis/]Zeltser's List

 - Free automated sandboxes and services, compiled by Lenny Zeltser.